diff --git a/main.go b/main.go
index fa5e528..4b86754 100644
--- a/main.go
+++ b/main.go
@@ -835,6 +835,16 @@ func unlinkStale(targetPath, repo string) error {
 	}
 
 	repoPath := filepath.Join(repoAbs, rel)
+	if _, err := os.Stat(repoPath); errors.Is(err, os.ErrNotExist) {
+		if err := os.Remove(targetPath); err != nil {
+			return err
+		}
+		fmt.Printf("removed %s (missing repo file)\n", targetPath)
+		return nil
+	} else if err != nil {
+		return err
+	}
+
 	if err := os.Remove(targetPath); err != nil {
 		return err
 	}