diff --git a/frontend/src/components/fileManager/FileHistoryGroup.tsx b/frontend/src/components/fileManager/FileHistoryGroup.tsx
index 28411079a..0c0f16d65 100644
--- a/frontend/src/components/fileManager/FileHistoryGroup.tsx
+++ b/frontend/src/components/fileManager/FileHistoryGroup.tsx
@@ -10,7 +10,7 @@ interface FileHistoryGroupProps {
   isExpanded: boolean;
   onDownloadSingle: (file: StirlingFileStub) => void;
   onFileDoubleClick: (file: StirlingFileStub) => void;
-  onFileRemove: (index: number) => void;
+  onHistoryFileRemove: (file: StirlingFileStub) => void;
   isFileSupported: (fileName: string) => boolean;
 }
 
@@ -20,7 +20,7 @@ const FileHistoryGroup: React.FC<FileHistoryGroupProps> = ({
   isExpanded,
   onDownloadSingle,
   onFileDoubleClick,
-  onFileRemove,
+  onHistoryFileRemove,
   isFileSupported,
 }) => {
   const { t } = useTranslation();
@@ -44,14 +44,14 @@ const FileHistoryGroup: React.FC<FileHistoryGroupProps> = ({
         </Group>
 
         <Box ml="md">
-          {sortedHistory.map((historyFile, index) => (
+          {sortedHistory.map((historyFile, _index) => (
             <FileListItem
               key={`history-${historyFile.id}-${historyFile.versionNumber || 1}`}
               file={historyFile}
               isSelected={false} // History files are not selectable
               isSupported={isFileSupported(historyFile.name)}
               onSelect={() => {}} // No selection for history files
-              onRemove={() => onFileRemove(index)} // Pass through remove handler
+              onRemove={() => onHistoryFileRemove(historyFile)} // Remove specific history file
               onDownload={() => onDownloadSingle(historyFile)}
               onDoubleClick={() => onFileDoubleClick(historyFile)}
               isHistoryFile={true} // This enables "Add to Recents" in menu
diff --git a/frontend/src/components/fileManager/FileListArea.tsx b/frontend/src/components/fileManager/FileListArea.tsx
index 87684baf0..842d0bf0e 100644
--- a/frontend/src/components/fileManager/FileListArea.tsx
+++ b/frontend/src/components/fileManager/FileListArea.tsx
@@ -25,6 +25,7 @@ const FileListArea: React.FC<FileListAreaProps> = ({
     loadedHistoryFiles,
     onFileSelect,
     onFileRemove,
+    onHistoryFileRemove,
     onFileDoubleClick,
     onDownloadSingle,
     isFileSupported,
@@ -78,7 +79,7 @@ const FileListArea: React.FC<FileListAreaProps> = ({
                     isExpanded={isExpanded}
                     onDownloadSingle={onDownloadSingle}
                     onFileDoubleClick={onFileDoubleClick}
-                    onFileRemove={onFileRemove}
+                    onHistoryFileRemove={onHistoryFileRemove}
                     isFileSupported={isFileSupported}
                   />
                 </React.Fragment>
diff --git a/frontend/src/contexts/FileManagerContext.tsx b/frontend/src/contexts/FileManagerContext.tsx
index 5499790a6..fba0cec5e 100644
--- a/frontend/src/contexts/FileManagerContext.tsx
+++ b/frontend/src/contexts/FileManagerContext.tsx
@@ -24,6 +24,7 @@ interface FileManagerContextValue {
   onLocalFileClick: () => void;
   onFileSelect: (file: StirlingFileStub, index: number, shiftKey?: boolean) => void;
   onFileRemove: (index: number) => void;
+  onHistoryFileRemove: (file: StirlingFileStub) => void;
   onFileDoubleClick: (file: StirlingFileStub) => void;
   onOpenFiles: () => void;
   onSearchChange: (value: string) => void;
@@ -172,7 +173,7 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
 
   // Helper function to safely determine which files can be deleted
   const getSafeFilesToDelete = useCallback((
-    leafFileIds: string[],
+    fileIds: string[],
     allStoredStubs: StirlingFileStub[]
   ): string[] => {
     const fileMap = new Map(allStoredStubs.map(f => [f.id as string, f]));
@@ -180,7 +181,7 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
     const filesToPreserve = new Set<string>();
 
     // First, identify all files in the lineages of the leaf files being deleted
-    for (const leafFileId of leafFileIds) {
+    for (const leafFileId of fileIds) {
       const currentFile = fileMap.get(leafFileId);
       if (!currentFile) continue;
 
@@ -206,7 +207,7 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
       const fileOriginalId = file.originalFileId || file.id;
 
       // If this file is a leaf node (not being deleted) and its lineage overlaps with files we want to delete
-      if (file.isLeaf !== false && !leafFileIds.includes(file.id)) {
+      if (file.isLeaf !== false && !fileIds.includes(file.id)) {
         // Find all files in this preserved lineage
         const preservedChainFiles = allStoredStubs.filter((chainFile: StirlingFileStub) =>
           (chainFile.originalFileId || chainFile.id) === fileOriginalId
@@ -287,6 +288,46 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
     }
   }, [filteredFiles, onFileRemove, refreshRecentFiles, getSafeFilesToDelete]);
 
+  // Handle deletion of specific history files (not index-based)
+  const handleHistoryFileRemove = useCallback(async (fileToRemove: StirlingFileStub) => {
+    const deletedFileId = fileToRemove.id;
+
+    // Clear from expanded state to prevent ghost entries
+    setExpandedFileIds(prev => {
+      const newExpanded = new Set(prev);
+      newExpanded.delete(deletedFileId);
+      return newExpanded;
+    });
+
+    // Clear from history cache - remove all files in the chain
+    setLoadedHistoryFiles(prev => {
+      const newCache = new Map(prev);
+
+      // Remove cache entries for all deleted files
+      newCache.delete(deletedFileId);
+
+      // Also remove deleted files from any other file's history cache
+      for (const [mainFileId, historyFiles] of newCache.entries()) {
+        const filteredHistory = historyFiles.filter(histFile => deletedFileId != histFile.id);
+        if (filteredHistory.length !== historyFiles.length) {
+          newCache.set(mainFileId, filteredHistory);
+        }
+      }
+
+      return newCache;
+    });
+
+    // Delete safe files from IndexedDB
+    try {
+        await fileStorage.deleteStirlingFile(deletedFileId);
+    } catch (error) {
+      console.error('Failed to delete files from chain:', error);
+    }
+
+    // Refresh to ensure consistent state
+    await refreshRecentFiles();
+  }, [filteredFiles, onFileRemove, refreshRecentFiles, getSafeFilesToDelete]);
+
   const handleFileDoubleClick = useCallback((file: StirlingFileStub) => {
     if (isFileSupported(file.name)) {
       onRecentFilesSelected([file]);
@@ -540,6 +581,7 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
     onLocalFileClick: handleLocalFileClick,
     onFileSelect: handleFileSelect,
     onFileRemove: handleFileRemove,
+    onHistoryFileRemove: handleHistoryFileRemove,
     onFileDoubleClick: handleFileDoubleClick,
     onOpenFiles: handleOpenFiles,
     onSearchChange: handleSearchChange,