diff --git a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileList.tsx b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileList.tsx
index 5cb95c19..514de40e 100644
--- a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileList.tsx
+++ b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileList.tsx
@@ -2,16 +2,18 @@ import fileListStyles from './fileList.module.scss';
 import { useSelector } from 'react-redux';
 import { AppDispatch, RootState, store as globalStore, useAppDispatch } from '../../../../redux';
 import { useEffect } from 'react';
-import { FileListElementTypeType } from '../../../../types/data/fileListType.ts';
+import { FileTreeElementTypeType } from '../../../../types/data/fileListType.ts';
 import { filterFileTree, generateFileTree } from './fileListUtilities/fileTreeUtilities.tsx';
 import FileListFolder from './fileListElements/fileListFolder.tsx';
 import { DatabaseSettingsDataPluginType } from '../../../../types/settings/databaseSettingsType.ts';
 import DataPluginStorage from '../../../../utils/dataPluginStorage.ts';
 import { setFileList, setFilesDataPluginId } from '../../../../redux/reducer/data/filesReducer.ts';
+import { DataPluginFile } from '../../../../plugins/interfaces/dataPluginInterfaces/dataPluginFiles.ts';
 
 function FileList(props: { orientation?: string; search: string }) {
   const dispatch: AppDispatch = useAppDispatch();
   const currentDataPlugins = useSelector((state: RootState) => state.settings.database.dataPlugins);
+  const fileTrees = useSelector((state: RootState) => state.files.fileTrees);
   const fileLists = useSelector((state: RootState) => state.files.fileLists);
   const fileCounts = useSelector((state: RootState) => state.files.fileCounts);
 
@@ -29,15 +31,20 @@ function FileList(props: { orientation?: string; search: string }) {
                 dispatch(
                   setFileList({
                     dataPluginId: dP.id !== undefined ? dP.id : -1,
-                    files: {
+                    fileTree: {
                       name: '/',
-                      type: FileListElementTypeType.Folder,
+                      type: FileTreeElementTypeType.Folder,
                       children: generateFileTree(files),
                       checked: true,
                       foldedOut: true,
                       isRoot: true,
                     },
-                    fileCount: files.length,
+                    files: files.map((f: DataPluginFile) => {
+                      return {
+                        element: f,
+                        checked: true,
+                      };
+                    }),
                   }),
                 ),
               )
@@ -68,6 +75,7 @@ function FileList(props: { orientation?: string; search: string }) {
     }
   });
 
+  console.log(fileLists[filesDataPluginId]);
   return (
     <>
       <div
@@ -79,8 +87,8 @@ function FileList(props: { orientation?: string; search: string }) {
         }>
         <div>{fileCounts[filesDataPluginId]} Files indexed</div>
         <div>
-          {fileLists[filesDataPluginId] ? (
-            <FileListFolder folder={filterFileTree(fileLists[filesDataPluginId],props.search)} foldedOut={true}></FileListFolder>
+          {fileTrees[filesDataPluginId] ? (
+            <FileListFolder folder={filterFileTree(fileTrees[filesDataPluginId], props.search)} foldedOut={true}></FileListFolder>
           ) : (
             <span className="loading loading-spinner loading-xs text-accent"></span>
           )}
diff --git a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFile.tsx b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFile.tsx
index 5d84a1e1..df87fc4e 100644
--- a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFile.tsx
+++ b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFile.tsx
@@ -1,11 +1,11 @@
 import fileListElementsStyles from './fileListElements.module.scss';
-import { FileListElementType } from '../../../../../types/data/fileListType.ts';
+import { FileTreeElementType } from '../../../../../types/data/fileListType.ts';
 import FileIcon from '../../../../../assets/file_gray.svg';
 import { updateFileListElement } from '../../../../../redux/reducer/data/filesReducer.ts';
 import { AppDispatch, useAppDispatch } from '../../../../../redux';
 import { formatName } from '../fileListUtilities/fileTreeUtilities.tsx';
 
-function FileListFile(props: { file: FileListElementType }) {
+function FileListFile(props: { file: FileTreeElementType }) {
   const dispatch: AppDispatch = useAppDispatch();
   return (
     <>
diff --git a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFolder.tsx b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFolder.tsx
index 1ab93948..c85aa782 100644
--- a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFolder.tsx
+++ b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListElements/fileListFolder.tsx
@@ -1,5 +1,5 @@
 import fileListElementsStyles from './fileListElements.module.scss';
-import { FileListElementType, FileListElementTypeType } from '../../../../../types/data/fileListType.ts';
+import { FileTreeElementType, FileTreeElementTypeType } from '../../../../../types/data/fileListType.ts';
 import FolderIcon from '../../../../../assets/folder_gray.svg';
 import FolderOpenIcon from '../../../../../assets/folder_open_gray.svg';
 import FileListFile from './fileListFile.tsx';
@@ -7,7 +7,7 @@ import { AppDispatch, useAppDispatch } from '../../../../../redux';
 import { updateFileListElement } from '../../../../../redux/reducer/data/filesReducer.ts';
 import { formatName } from '../fileListUtilities/fileTreeUtilities.tsx';
 
-function FileListFolder(props: { folder: FileListElementType; foldedOut: boolean }) {
+function FileListFolder(props: { folder: FileTreeElementType; foldedOut: boolean }) {
   const dispatch: AppDispatch = useAppDispatch();
 
   return (
@@ -43,9 +43,9 @@ function FileListFolder(props: { folder: FileListElementType; foldedOut: boolean
                   }
                   return 0;
                 })
-                .sort((e) => (e.type === FileListElementTypeType.Folder ? -1 : 1))
+                .sort((e) => (e.type === FileTreeElementTypeType.Folder ? -1 : 1))
                 .map((element, i) => {
-                  if (element.type === FileListElementTypeType.Folder && element.children) {
+                  if (element.type === FileTreeElementTypeType.Folder && element.children) {
                     return <FileListFolder key={`fileListElement${i}`} folder={element} foldedOut={false}></FileListFolder>;
                   } else {
                     return <FileListFile key={`fileListElement${i}`} file={element}></FileListFile>;
diff --git a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListUtilities/fileTreeUtilities.tsx b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListUtilities/fileTreeUtilities.tsx
index e76e1916..f6156fff 100644
--- a/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListUtilities/fileTreeUtilities.tsx
+++ b/binocular-frontend-new/src/components/tabs/fileTree/fileList/fileListUtilities/fileTreeUtilities.tsx
@@ -1,8 +1,8 @@
-import { FileListElementType, FileListElementTypeType } from '../../../../../types/data/fileListType.ts';
+import { FileTreeElementType, FileTreeElementTypeType } from '../../../../../types/data/fileListType.ts';
 import { DataPluginFile } from '../../../../../plugins/interfaces/dataPluginInterfaces/dataPluginFiles.ts';
 import fileListElementsStyles from '../fileListElements/fileListElements.module.scss';
 
-export function generateFileTree(files: DataPluginFile[]): FileListElementType[] {
+export function generateFileTree(files: DataPluginFile[]): FileTreeElementType[] {
   return convertData(files).content;
 }
 
@@ -18,7 +18,7 @@ function convertData(files: DataPluginFile[]) {
   return convertedData;
 }
 
-function genPathObjectString(convertedData: FileListElementType[], pathParts: string[], file: DataPluginFile, id: number) {
+function genPathObjectString(convertedData: FileTreeElementType[], pathParts: string[], file: DataPluginFile, id: number) {
   const currElm = pathParts.shift();
   id++;
   if (currElm) {
@@ -26,7 +26,7 @@ function genPathObjectString(convertedData: FileListElementType[], pathParts: st
       convertedData.push({
         name: currElm,
         id: id,
-        type: FileListElementTypeType.File,
+        type: FileTreeElementTypeType.File,
         checked: true,
         element: file,
         foldedOut: false,
@@ -38,7 +38,7 @@ function genPathObjectString(convertedData: FileListElementType[], pathParts: st
         elem = {
           name: currElm,
           id: id,
-          type: FileListElementTypeType.Folder,
+          type: FileTreeElementTypeType.Folder,
           children: [],
           checked: true,
           foldedOut: false,
@@ -58,21 +58,21 @@ function genPathObjectString(convertedData: FileListElementType[], pathParts: st
   return id;
 }
 
-export function filterFileTree(fileTree: FileListElementType, search: string): FileListElementType {
+export function filterFileTree(fileTree: FileTreeElementType, search: string): FileTreeElementType {
   if (fileTree.children) {
     return {
       ...fileTree,
       searchTerm: search,
       children: fileTree.children
         ?.map((child) => {
-          if (child.type === FileListElementTypeType.Folder) {
+          if (child.type === FileTreeElementTypeType.Folder) {
             return filterFileTree(child, search);
           } else {
             return { ...child, searchTerm: search };
           }
         })
         .filter((child) => {
-          if (child.type === FileListElementTypeType.Folder && child.children) {
+          if (child.type === FileTreeElementTypeType.Folder && child.children) {
             return child.children.length > 0;
           }
           return child.element?.path.toLowerCase().includes(search.toLowerCase());
diff --git a/binocular-frontend-new/src/redux/reducer/data/filesReducer.ts b/binocular-frontend-new/src/redux/reducer/data/filesReducer.ts
index 76c33d4a..d43f94b1 100644
--- a/binocular-frontend-new/src/redux/reducer/data/filesReducer.ts
+++ b/binocular-frontend-new/src/redux/reducer/data/filesReducer.ts
@@ -1,14 +1,16 @@
 import { createSlice, PayloadAction } from '@reduxjs/toolkit';
 import Config from '../../../config.ts';
-import { FileListElementType } from '../../../types/data/fileListType.ts';
+import { FileListElementType, FileTreeElementType } from '../../../types/data/fileListType.ts';
 
 export interface FilesInitialState {
-  fileLists: { [id: number]: FileListElementType };
+  fileTrees: { [id: number]: FileTreeElementType };
+  fileLists: { [id: number]: FileListElementType[] };
   fileCounts: { [id: number]: number };
   dataPluginId: number | undefined;
 }
 
 const initialState: FilesInitialState = {
+  fileTrees: {},
   fileLists: {},
   fileCounts: {},
   dataPluginId: undefined,
@@ -26,11 +28,12 @@ export const filesSlice = createSlice({
     }
   },
   reducers: {
-    setFileList: (state, action: PayloadAction<{ dataPluginId: number; files: FileListElementType; fileCount: number }>) => {
+    setFileList: (state, action: PayloadAction<{ dataPluginId: number; fileTree: FileTreeElementType; files: FileListElementType[] }>) => {
       const fileCount: number = state.fileCounts[action.payload.dataPluginId];
-      if (fileCount === undefined || fileCount !== action.payload.fileCount) {
+      if (fileCount === undefined || fileCount !== action.payload.files.length) {
+        state.fileTrees[action.payload.dataPluginId] = action.payload.fileTree;
+        state.fileCounts[action.payload.dataPluginId] = action.payload.files.length;
         state.fileLists[action.payload.dataPluginId] = action.payload.files;
-        state.fileCounts[action.payload.dataPluginId] = action.payload.fileCount;
       }
       localStorage.setItem(`${filesSlice.name}StateV${Config.localStorageVersion}`, JSON.stringify(state));
     },
@@ -38,9 +41,14 @@ export const filesSlice = createSlice({
       state.dataPluginId = action.payload;
       localStorage.setItem(`${filesSlice.name}StateV${Config.localStorageVersion}`, JSON.stringify(state));
     },
-    updateFileListElement: (state, action: PayloadAction<FileListElementType>) => {
-      state.fileLists[state.dataPluginId] = updateFileListElementRecursive(state.fileLists[state.dataPluginId], action.payload);
-
+    updateFileListElement: (state, action: PayloadAction<FileTreeElementType>) => {
+      const updatedPaths: string[] = updateFileTreeRecursive(state.fileTrees[state.dataPluginId], action.payload);
+      state.fileLists[state.dataPluginId] = state.fileLists[state.dataPluginId].map((f: FileListElementType) => {
+        if (updatedPaths.includes(f.element.path)) {
+          f.checked = action.payload.checked;
+        }
+        return f;
+      });
       localStorage.setItem(`${filesSlice.name}StateV${Config.localStorageVersion}`, JSON.stringify(state));
     },
   },
@@ -49,24 +57,27 @@ export const filesSlice = createSlice({
 export const { setFilesDataPluginId, setFileList, updateFileListElement } = filesSlice.actions;
 export default filesSlice.reducer;
 
-function updateFileListElementRecursive(
-  fileList: FileListElementType,
-  element: FileListElementType,
-  checked?: boolean,
-): FileListElementType {
-  if (fileList.children) {
-    fileList.children = fileList.children.map((f: FileListElementType) => {
+function updateFileTreeRecursive(fileTree: FileTreeElementType, element: FileTreeElementType, checked?: boolean): string[] {
+  const updatedPaths: string[] = [];
+  if (fileTree.children) {
+    fileTree.children = fileTree.children.map((f: FileTreeElementType) => {
       let elementChecked = checked;
       if (f.id === element.id) {
+        if (f.element?.path && !updatedPaths.includes(f.element.path)) {
+          updatedPaths.push(f.element.path);
+        }
         elementChecked = element.checked;
         f.foldedOut = element.foldedOut;
       }
       if (elementChecked !== undefined) {
+        if (f.element?.path && !updatedPaths.includes(f.element.path)) {
+          updatedPaths.push(f.element.path);
+        }
         f.checked = elementChecked;
       }
-      updateFileListElementRecursive(f, element, elementChecked);
+      updatedPaths.push(...updateFileTreeRecursive(f, element, elementChecked));
       return f;
     });
   }
-  return fileList;
+  return updatedPaths;
 }
diff --git a/binocular-frontend-new/src/types/data/fileListType.ts b/binocular-frontend-new/src/types/data/fileListType.ts
index 95be2e06..592ed048 100644
--- a/binocular-frontend-new/src/types/data/fileListType.ts
+++ b/binocular-frontend-new/src/types/data/fileListType.ts
@@ -1,18 +1,22 @@
 import { DataPluginFile } from '../../plugins/interfaces/dataPluginInterfaces/dataPluginFiles.ts';
 
 export interface FileListElementType {
+  element: DataPluginFile;
+  checked: boolean;
+}
+export interface FileTreeElementType {
   name: string;
   id?: number;
-  type: FileListElementTypeType;
+  type: FileTreeElementTypeType;
   element?: DataPluginFile;
-  children?: FileListElementType[];
+  children?: FileTreeElementType[];
   searchTerm?: string;
   checked: boolean;
   foldedOut: boolean;
   isRoot: boolean;
 }
 
-export enum FileListElementTypeType {
+export enum FileTreeElementTypeType {
   Folder,
   File,
 }