diff --git a/cmd/root_test.go b/cmd/root_test.go
index e76043e..ffc8286 100644
--- a/cmd/root_test.go
+++ b/cmd/root_test.go
@@ -4,6 +4,7 @@ import (
 	"bytes"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/stretchr/testify/suite"
@@ -105,9 +106,19 @@ func (suite *CLITestSuite) TestAddCommand() {
 	suite.NoError(err)
 	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
 
-	// Verify file exists in repo
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".bashrc")
-	suite.FileExists(repoFile)
+	// Verify some file exists in repo with .bashrc in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.NoError(err)
+
+	found := false
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".bashrc") && entry.Name() != ".lnk" {
+			found = true
+			break
+		}
+	}
+	suite.True(found, "Repository should contain a file with .bashrc in the name")
 }
 
 func (suite *CLITestSuite) TestRemoveCommand() {
@@ -325,9 +336,92 @@ func (suite *CLITestSuite) TestAddDirectory() {
 	suite.NoError(err)
 	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
 
-	// Verify directory exists in repo
-	repoDir := filepath.Join(suite.tempDir, "lnk", ".config")
-	suite.DirExists(repoDir)
+	// Verify some directory exists in repo with .config in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.NoError(err)
+
+	found := false
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".config") && entry.Name() != ".lnk" {
+			found = true
+			break
+		}
+	}
+	suite.True(found, "Repository should contain a directory with .config in the name")
+}
+
+func (suite *CLITestSuite) TestSameBasenameFilesBug() {
+	// Initialize repository
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Create two directories with files having the same basename
+	dirA := filepath.Join(suite.tempDir, "a")
+	dirB := filepath.Join(suite.tempDir, "b")
+	err = os.MkdirAll(dirA, 0755)
+	suite.Require().NoError(err)
+	err = os.MkdirAll(dirB, 0755)
+	suite.Require().NoError(err)
+
+	// Create files with same basename but different content
+	fileA := filepath.Join(dirA, "config.json")
+	fileB := filepath.Join(dirB, "config.json")
+	contentA := `{"name": "config_a"}`
+	contentB := `{"name": "config_b"}`
+
+	err = os.WriteFile(fileA, []byte(contentA), 0644)
+	suite.Require().NoError(err)
+	err = os.WriteFile(fileB, []byte(contentB), 0644)
+	suite.Require().NoError(err)
+
+	// Add first file
+	err = suite.runCommand("add", fileA)
+	suite.NoError(err)
+	suite.stdout.Reset()
+
+	// Verify first file content is preserved
+	content, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	suite.Equal(contentA, string(content), "First file should preserve its original content")
+
+	// Add second file with same basename - this should work correctly
+	err = suite.runCommand("add", fileB)
+	suite.NoError(err, "Adding second file with same basename should work")
+
+	// CORRECT BEHAVIOR: Both files should preserve their original content
+	contentAfterAddA, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	contentAfterAddB, err := os.ReadFile(fileB)
+	suite.NoError(err)
+
+	suite.Equal(contentA, string(contentAfterAddA), "First file should keep its original content")
+	suite.Equal(contentB, string(contentAfterAddB), "Second file should keep its original content")
+
+	// Both files should be removable independently
+	suite.stdout.Reset()
+	err = suite.runCommand("rm", fileA)
+	suite.NoError(err, "First file should be removable")
+
+	// Verify output shows removal
+	output := suite.stdout.String()
+	suite.Contains(output, "Removed config.json from lnk")
+
+	// Verify first file is restored with correct content
+	restoredContentA, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	suite.Equal(contentA, string(restoredContentA), "Restored first file should have original content")
+
+	// Second file should still be removable without errors
+	suite.stdout.Reset()
+	err = suite.runCommand("rm", fileB)
+	suite.NoError(err, "Second file should also be removable without errors")
+
+	// Verify second file is restored with correct content
+	restoredContentB, err := os.ReadFile(fileB)
+	suite.NoError(err)
+	suite.Equal(contentB, string(restoredContentB), "Restored second file should have original content")
 }
 
 func TestCLISuite(t *testing.T) {
diff --git a/internal/core/lnk.go b/internal/core/lnk.go
index 7e0700f..269da93 100644
--- a/internal/core/lnk.go
+++ b/internal/core/lnk.go
@@ -43,6 +43,41 @@ func getRepoPath() string {
 	return filepath.Join(xdgConfig, "lnk")
 }
 
+// generateRepoName creates a unique repository filename from a relative path
+func generateRepoName(relativePath string) string {
+	// Replace slashes and backslashes with underscores to create valid filename
+	repoName := strings.ReplaceAll(relativePath, "/", "_")
+	repoName = strings.ReplaceAll(repoName, "\\", "_")
+	return repoName
+}
+
+// getRelativePath converts an absolute path to a relative path from home directory
+func getRelativePath(absPath string) (string, error) {
+	homeDir, err := os.UserHomeDir()
+	if err != nil {
+		return "", fmt.Errorf("failed to get home directory: %w", err)
+	}
+
+	// Check if the file is under home directory
+	relPath, err := filepath.Rel(homeDir, absPath)
+	if err != nil {
+		return "", fmt.Errorf("failed to get relative path: %w", err)
+	}
+
+	// If the relative path starts with "..", the file is outside home directory
+	// In this case, use the absolute path as relative (without the leading slash)
+	if strings.HasPrefix(relPath, "..") {
+		// Use absolute path but remove leading slash and drive letter (for cross-platform)
+		cleanPath := strings.TrimPrefix(absPath, "/")
+		if len(cleanPath) > 1 && cleanPath[1] == ':' {
+			// Windows drive letter, keep as is
+		}
+		return cleanPath, nil
+	}
+
+	return relPath, nil
+}
+
 // Init initializes the lnk repository
 func (l *Lnk) Init() error {
 	return l.InitWithRemote("")
@@ -109,9 +144,26 @@ func (l *Lnk) Add(filePath string) error {
 		return fmt.Errorf("failed to get absolute path: %w", err)
 	}
 
-	// Calculate destination path in repo
-	basename := filepath.Base(absPath)
-	destPath := filepath.Join(l.repoPath, basename)
+	// Get relative path for tracking
+	relativePath, err := getRelativePath(absPath)
+	if err != nil {
+		return fmt.Errorf("failed to get relative path: %w", err)
+	}
+
+	// Generate unique repository name from relative path
+	repoName := generateRepoName(relativePath)
+	destPath := filepath.Join(l.repoPath, repoName)
+
+	// Check if this relative path is already managed
+	managedItems, err := l.getManagedItems()
+	if err != nil {
+		return fmt.Errorf("failed to get managed items: %w", err)
+	}
+	for _, item := range managedItems {
+		if item == relativePath {
+			return fmt.Errorf("❌ File is already managed by lnk: \033[31m%s\033[0m", relativePath)
+		}
+	}
 
 	// Check if it's a directory or file
 	info, err := os.Stat(absPath)
@@ -141,8 +193,8 @@ func (l *Lnk) Add(filePath string) error {
 		return fmt.Errorf("failed to create symlink: %w", err)
 	}
 
-	// Add to .lnk tracking file
-	if err := l.addManagedItem(absPath); err != nil {
+	// Add to .lnk tracking file using relative path
+	if err := l.addManagedItem(relativePath); err != nil {
 		// Try to restore the original state if tracking fails
 		_ = os.Remove(absPath) // Ignore error in cleanup
 		if info.IsDir() {
@@ -154,10 +206,10 @@ func (l *Lnk) Add(filePath string) error {
 	}
 
 	// Add both the item and .lnk file to git in a single commit
-	if err := l.git.Add(basename); err != nil {
+	if err := l.git.Add(repoName); err != nil {
 		// Try to restore the original state if git add fails
-		_ = os.Remove(absPath)           // Ignore error in cleanup
-		_ = l.removeManagedItem(absPath) // Ignore error in cleanup
+		_ = os.Remove(absPath)                // Ignore error in cleanup
+		_ = l.removeManagedItem(relativePath) // Ignore error in cleanup
 		if info.IsDir() {
 			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
 		} else {
@@ -169,8 +221,8 @@ func (l *Lnk) Add(filePath string) error {
 	// Add .lnk file to the same commit
 	if err := l.git.Add(".lnk"); err != nil {
 		// Try to restore the original state if git add fails
-		_ = os.Remove(absPath)           // Ignore error in cleanup
-		_ = l.removeManagedItem(absPath) // Ignore error in cleanup
+		_ = os.Remove(absPath)                // Ignore error in cleanup
+		_ = l.removeManagedItem(relativePath) // Ignore error in cleanup
 		if info.IsDir() {
 			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
 		} else {
@@ -180,10 +232,11 @@ func (l *Lnk) Add(filePath string) error {
 	}
 
 	// Commit both changes together
+	basename := filepath.Base(relativePath)
 	if err := l.git.Commit(fmt.Sprintf("lnk: added %s", basename)); err != nil {
 		// Try to restore the original state if commit fails
-		_ = os.Remove(absPath)           // Ignore error in cleanup
-		_ = l.removeManagedItem(absPath) // Ignore error in cleanup
+		_ = os.Remove(absPath)                // Ignore error in cleanup
+		_ = l.removeManagedItem(relativePath) // Ignore error in cleanup
 		if info.IsDir() {
 			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
 		} else {
@@ -208,6 +261,29 @@ func (l *Lnk) Remove(filePath string) error {
 		return err
 	}
 
+	// Get relative path for tracking
+	relativePath, err := getRelativePath(absPath)
+	if err != nil {
+		return fmt.Errorf("failed to get relative path: %w", err)
+	}
+
+	// Check if this relative path is managed
+	managedItems, err := l.getManagedItems()
+	if err != nil {
+		return fmt.Errorf("failed to get managed items: %w", err)
+	}
+
+	found := false
+	for _, item := range managedItems {
+		if item == relativePath {
+			found = true
+			break
+		}
+	}
+	if !found {
+		return fmt.Errorf("❌ File is not managed by lnk: \033[31m%s\033[0m", relativePath)
+	}
+
 	// Get the target path in the repository
 	target, err := os.Readlink(absPath)
 	if err != nil {
@@ -219,7 +295,7 @@ func (l *Lnk) Remove(filePath string) error {
 		target = filepath.Join(filepath.Dir(absPath), target)
 	}
 
-	basename := filepath.Base(target)
+	repoName := filepath.Base(target)
 
 	// Check if target is a directory or file
 	info, err := os.Stat(target)
@@ -232,13 +308,13 @@ func (l *Lnk) Remove(filePath string) error {
 		return fmt.Errorf("failed to remove symlink: %w", err)
 	}
 
-	// Remove from .lnk tracking file
-	if err := l.removeManagedItem(absPath); err != nil {
+	// Remove from .lnk tracking file using relative path
+	if err := l.removeManagedItem(relativePath); err != nil {
 		return fmt.Errorf("failed to update tracking file: %w", err)
 	}
 
 	// Remove from Git first (while the item is still in the repository)
-	if err := l.git.Remove(basename); err != nil {
+	if err := l.git.Remove(repoName); err != nil {
 		return fmt.Errorf("failed to remove from git: %w", err)
 	}
 
@@ -248,6 +324,7 @@ func (l *Lnk) Remove(filePath string) error {
 	}
 
 	// Commit both changes together
+	basename := filepath.Base(relativePath)
 	if err := l.git.Commit(fmt.Sprintf("lnk: removed %s", basename)); err != nil {
 		return fmt.Errorf("failed to commit changes: %w", err)
 	}
@@ -356,34 +433,41 @@ func (l *Lnk) Pull() ([]string, error) {
 func (l *Lnk) RestoreSymlinks() ([]string, error) {
 	var restored []string
 
-	// Get managed items from .lnk file
+	// Get managed items from .lnk file (now containing relative paths)
 	managedItems, err := l.getManagedItems()
 	if err != nil {
 		return nil, fmt.Errorf("failed to get managed items: %w", err)
 	}
 
-	for _, itemName := range managedItems {
-		repoItem := filepath.Join(l.repoPath, itemName)
+	homeDir, err := os.UserHomeDir()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get home directory: %w", err)
+	}
+
+	for _, relativePath := range managedItems {
+		// Generate repository name from relative path
+		repoName := generateRepoName(relativePath)
+		repoItem := filepath.Join(l.repoPath, repoName)
 
 		// Check if item exists in repository
 		if _, err := os.Stat(repoItem); os.IsNotExist(err) {
 			continue // Skip missing items
 		}
 
-		// Determine where the symlink should be
-		// For config files, we'll place them in the user's home directory
-		homeDir, err := os.UserHomeDir()
-		if err != nil {
-			return nil, fmt.Errorf("failed to get home directory: %w", err)
-		}
-
-		symlinkPath := filepath.Join(homeDir, itemName)
+		// Determine where the symlink should be created
+		symlinkPath := filepath.Join(homeDir, relativePath)
 
 		// Check if symlink already exists and is correct
 		if l.isValidSymlink(symlinkPath, repoItem) {
 			continue
 		}
 
+		// Ensure parent directory exists
+		symlinkDir := filepath.Dir(symlinkPath)
+		if err := os.MkdirAll(symlinkDir, 0755); err != nil {
+			return nil, fmt.Errorf("failed to create directory %s: %w", symlinkDir, err)
+		}
+
 		// Remove existing file/symlink if it exists
 		if _, err := os.Lstat(symlinkPath); err == nil {
 			if err := os.RemoveAll(symlinkPath); err != nil {
@@ -393,10 +477,10 @@ func (l *Lnk) RestoreSymlinks() ([]string, error) {
 
 		// Create symlink
 		if err := l.fs.CreateSymlink(repoItem, symlinkPath); err != nil {
-			return nil, fmt.Errorf("failed to create symlink for %s: %w", itemName, err)
+			return nil, fmt.Errorf("failed to create symlink for %s: %w", relativePath, err)
 		}
 
-		restored = append(restored, itemName)
+		restored = append(restored, relativePath)
 	}
 
 	return restored, nil
@@ -470,25 +554,22 @@ func (l *Lnk) getManagedItems() ([]string, error) {
 }
 
 // addManagedItem adds an item to the .lnk tracking file
-func (l *Lnk) addManagedItem(itemPath string) error {
+func (l *Lnk) addManagedItem(relativePath string) error {
 	// Get current items
 	items, err := l.getManagedItems()
 	if err != nil {
 		return fmt.Errorf("failed to get managed items: %w", err)
 	}
 
-	// Get the basename for storage
-	basename := filepath.Base(itemPath)
-
 	// Check if already exists
 	for _, item := range items {
-		if item == basename {
+		if item == relativePath {
 			return nil // Already managed
 		}
 	}
 
-	// Add new item
-	items = append(items, basename)
+	// Add new item using relative path
+	items = append(items, relativePath)
 
 	// Sort for consistent ordering
 	sort.Strings(items)
@@ -497,20 +578,17 @@ func (l *Lnk) addManagedItem(itemPath string) error {
 }
 
 // removeManagedItem removes an item from the .lnk tracking file
-func (l *Lnk) removeManagedItem(itemPath string) error {
+func (l *Lnk) removeManagedItem(relativePath string) error {
 	// Get current items
 	items, err := l.getManagedItems()
 	if err != nil {
 		return fmt.Errorf("failed to get managed items: %w", err)
 	}
 
-	// Get the basename for removal
-	basename := filepath.Base(itemPath)
-
-	// Remove item
+	// Remove item using relative path
 	var newItems []string
 	for _, item := range items {
-		if item != basename {
+		if item != relativePath {
 			newItems = append(newItems, item)
 		}
 	}
diff --git a/internal/core/lnk_test.go b/internal/core/lnk_test.go
index b283de2..dc899da 100644
--- a/internal/core/lnk_test.go
+++ b/internal/core/lnk_test.go
@@ -82,7 +82,19 @@ func (suite *CoreTestSuite) TestCoreFileOperations() {
 	suite.Require().NoError(err)
 	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
 
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".bashrc")
+	// The repository file will have a generated name based on the relative path
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.Require().NoError(err)
+
+	var repoFile string
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".bashrc") && entry.Name() != ".lnk" {
+			repoFile = filepath.Join(lnkDir, entry.Name())
+			break
+		}
+	}
+	suite.NotEmpty(repoFile, "Repository should contain a file with .bashrc in the name")
 	suite.FileExists(repoFile)
 
 	// Verify content is preserved
@@ -129,8 +141,19 @@ func (suite *CoreTestSuite) TestCoreDirectoryOperations() {
 	suite.Require().NoError(err)
 	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
 
-	// Verify directory exists in repo
-	repoDir := filepath.Join(suite.tempDir, "lnk", "testdir")
+	// Check that some repository directory exists with testdir in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.Require().NoError(err)
+
+	var repoDir string
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), "testdir") && entry.Name() != ".lnk" {
+			repoDir = filepath.Join(lnkDir, entry.Name())
+			break
+		}
+	}
+	suite.NotEmpty(repoDir, "Repository should contain a directory with testdir in the name")
 	suite.DirExists(repoDir)
 
 	// Remove the directory
@@ -179,8 +202,12 @@ func (suite *CoreTestSuite) TestLnkFileTracking() {
 
 	lines := strings.Split(strings.TrimSpace(string(lnkContent)), "\n")
 	suite.Len(lines, 2)
-	suite.Contains(lines, ".bashrc")
-	suite.Contains(lines, ".ssh")
+
+	// The .lnk file now contains relative paths, not basenames
+	// Check that the content contains references to .bashrc and .ssh
+	content := string(lnkContent)
+	suite.Contains(content, ".bashrc", ".lnk file should contain reference to .bashrc")
+	suite.Contains(content, ".ssh", ".lnk file should contain reference to .ssh")
 
 	// Remove one item and verify tracking is updated
 	err = suite.lnk.Remove(testFile)
@@ -191,8 +218,10 @@ func (suite *CoreTestSuite) TestLnkFileTracking() {
 
 	lines = strings.Split(strings.TrimSpace(string(lnkContent)), "\n")
 	suite.Len(lines, 1)
-	suite.Contains(lines, ".ssh")
-	suite.NotContains(lines, ".bashrc")
+
+	content = string(lnkContent)
+	suite.Contains(content, ".ssh", ".lnk file should still contain reference to .ssh")
+	suite.NotContains(content, ".bashrc", ".lnk file should not contain reference to .bashrc after removal")
 }
 
 // Test XDG_CONFIG_HOME fallback
@@ -310,6 +339,147 @@ func (suite *CoreTestSuite) TestGitOperations() {
 	suite.Equal(0, status.Behind)
 }
 
+// Test edge case: files with same basename from different directories should be handled properly
+func (suite *CoreTestSuite) TestSameBasenameFilesOverwrite() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create two directories with files having the same basename
+	dirA := filepath.Join(suite.tempDir, "a")
+	dirB := filepath.Join(suite.tempDir, "b")
+	err = os.MkdirAll(dirA, 0755)
+	suite.Require().NoError(err)
+	err = os.MkdirAll(dirB, 0755)
+	suite.Require().NoError(err)
+
+	// Create files with same basename but different content
+	fileA := filepath.Join(dirA, "config.json")
+	fileB := filepath.Join(dirB, "config.json")
+	contentA := `{"name": "config_a"}`
+	contentB := `{"name": "config_b"}`
+
+	err = os.WriteFile(fileA, []byte(contentA), 0644)
+	suite.Require().NoError(err)
+	err = os.WriteFile(fileB, []byte(contentB), 0644)
+	suite.Require().NoError(err)
+
+	// Add first file
+	err = suite.lnk.Add(fileA)
+	suite.Require().NoError(err)
+
+	// Verify first file is managed correctly and preserves content
+	info, err := os.Lstat(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	symlinkContentA, err := os.ReadFile(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(contentA, string(symlinkContentA), "First file should preserve its original content")
+
+	// Add second file - this should work without overwriting the first
+	err = suite.lnk.Add(fileB)
+	suite.Require().NoError(err)
+
+	// Verify second file is managed
+	info, err = os.Lstat(fileB)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// CORRECT BEHAVIOR: Both files should preserve their original content
+	symlinkContentA, err = os.ReadFile(fileA)
+	suite.Require().NoError(err)
+	symlinkContentB, err := os.ReadFile(fileB)
+	suite.Require().NoError(err)
+
+	suite.Equal(contentA, string(symlinkContentA), "First file should keep its original content")
+	suite.Equal(contentB, string(symlinkContentB), "Second file should keep its original content")
+
+	// Both files should be removable independently
+	err = suite.lnk.Remove(fileA)
+	suite.Require().NoError(err, "First file should be removable")
+
+	// First file should be restored with correct content
+	info, err = os.Lstat(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink anymore
+
+	restoredContentA, err := os.ReadFile(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(contentA, string(restoredContentA), "Restored file should have original content")
+
+	// Second file should still be manageable and removable
+	err = suite.lnk.Remove(fileB)
+	suite.Require().NoError(err, "Second file should also be removable without errors")
+
+	// Second file should be restored with correct content
+	info, err = os.Lstat(fileB)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink anymore
+
+	restoredContentB, err := os.ReadFile(fileB)
+	suite.Require().NoError(err)
+	suite.Equal(contentB, string(restoredContentB), "Second restored file should have original content")
+}
+
+// Test another variant: adding files with same basename should work correctly
+func (suite *CoreTestSuite) TestSameBasenameSequentialAdd() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create subdirectories in different locations
+	configDir := filepath.Join(suite.tempDir, "config")
+	backupDir := filepath.Join(suite.tempDir, "backup")
+	err = os.MkdirAll(configDir, 0755)
+	suite.Require().NoError(err)
+	err = os.MkdirAll(backupDir, 0755)
+	suite.Require().NoError(err)
+
+	// Create files with same basename (.bashrc)
+	configBashrc := filepath.Join(configDir, ".bashrc")
+	backupBashrc := filepath.Join(backupDir, ".bashrc")
+
+	originalContent := "export PATH=/usr/local/bin:$PATH"
+	backupContent := "export PATH=/opt/bin:$PATH"
+
+	err = os.WriteFile(configBashrc, []byte(originalContent), 0644)
+	suite.Require().NoError(err)
+	err = os.WriteFile(backupBashrc, []byte(backupContent), 0644)
+	suite.Require().NoError(err)
+
+	// Add first .bashrc
+	err = suite.lnk.Add(configBashrc)
+	suite.Require().NoError(err)
+
+	// Add second .bashrc - should work without overwriting the first
+	err = suite.lnk.Add(backupBashrc)
+	suite.Require().NoError(err)
+
+	// Check .lnk tracking file should track both properly
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.Require().NoError(err)
+
+	// Both entries should be tracked and distinguishable
+	content := string(lnkContent)
+	suite.Contains(content, ".bashrc", "Both .bashrc files should be tracked")
+
+	// Both files should maintain their distinct content
+	content1, err := os.ReadFile(configBashrc)
+	suite.Require().NoError(err)
+	content2, err := os.ReadFile(backupBashrc)
+	suite.Require().NoError(err)
+
+	suite.Equal(originalContent, string(content1), "First file should keep original content")
+	suite.Equal(backupContent, string(content2), "Second file should keep its distinct content")
+
+	// Both should be removable independently
+	err = suite.lnk.Remove(configBashrc)
+	suite.Require().NoError(err, "First .bashrc should be removable")
+
+	err = suite.lnk.Remove(backupBashrc)
+	suite.Require().NoError(err, "Second .bashrc should be removable")
+}
+
 func TestCoreSuite(t *testing.T) {
 	suite.Run(t, new(CoreTestSuite))
 }