diff --git a/src/services/hidden_subtree.ts b/src/services/hidden_subtree.ts
index e4cdf49bd..211ef1052 100644
--- a/src/services/hidden_subtree.ts
+++ b/src/services/hidden_subtree.ts
@@ -6,7 +6,7 @@ import noteService from "./notes.js";
 import log from "./log.js";
 import migrationService from "./migration.js";
 import { t } from "i18next";
-import { getHelpHiddenSubtreeData } from "./in_app_help.js";
+import { cleanUpHelp, getHelpHiddenSubtreeData } from "./in_app_help.js";
 import buildLaunchBarConfig from "./hidden_subtree_launcherbar.js";
 
 const LBTPL_ROOT = "_lbTplRoot";
@@ -58,7 +58,7 @@ enum Command {
 
 let hiddenSubtreeDefinition: HiddenSubtreeItem;
 
-function buildHiddenSubtreeDefinition(): HiddenSubtreeItem {
+function buildHiddenSubtreeDefinition(helpSubtree: HiddenSubtreeItem[]): HiddenSubtreeItem {
     const launchbarConfig = buildLaunchBarConfig();
 
     return {
@@ -283,7 +283,7 @@ function buildHiddenSubtreeDefinition(): HiddenSubtreeItem {
                 title: t("hidden-subtree.user-guide"),
                 type: "book",
                 icon: "bx-help-circle",
-                children: getHelpHiddenSubtreeData(),
+                children: helpSubtree,
                 isExpanded: true
             }
         ]
@@ -301,11 +301,19 @@ function checkHiddenSubtree(force = false, extraOpts: CheckHiddenExtraOpts = {})
         return;
     }
 
+    const helpSubtree = getHelpHiddenSubtreeData();
     if (!hiddenSubtreeDefinition || force) {
-        hiddenSubtreeDefinition = buildHiddenSubtreeDefinition();
+        hiddenSubtreeDefinition = buildHiddenSubtreeDefinition(helpSubtree);
     }
 
     checkHiddenSubtreeRecursively("root", hiddenSubtreeDefinition, extraOpts);
+
+    try {
+        cleanUpHelp(helpSubtree);
+    } catch (e) {
+        // Non-critical operation should something go wrong.
+        console.error(e);
+    }
 }
 
 function checkHiddenSubtreeRecursively(parentNoteId: string, item: HiddenSubtreeItem, extraOpts: CheckHiddenExtraOpts = {}) {
diff --git a/src/services/in_app_help.ts b/src/services/in_app_help.ts
index fffbf7812..a090993c4 100644
--- a/src/services/in_app_help.ts
+++ b/src/services/in_app_help.ts
@@ -5,6 +5,8 @@ import type NoteMeta from "./meta/note_meta.js";
 import type { NoteMetaFile } from "./meta/note_meta.js";
 import { fileURLToPath } from "url";
 import { isDev } from "./utils.js";
+import type BNote from "../becca/entities/bnote.js";
+import becca from "../becca/becca.js";
 
 export function getHelpHiddenSubtreeData() {
     const srcRoot = path.join(path.dirname(fileURLToPath(import.meta.url)), "..");
@@ -98,3 +100,55 @@ function parseNoteMeta(noteMeta: NoteMeta, docNameRoot: string): HiddenSubtreeIt
 
     return item;
 }
+/**
+ * Iterates recursively through the help subtree that the user has and compares it against the definition
+ * to remove any notes that are no longer present in the latest version of the help.
+ *
+ * @param helpDefinition the hidden subtree definition for the help, to compare against the user's structure.
+ */
+export function cleanUpHelp(helpDefinition: HiddenSubtreeItem[]) {
+    function getFlatIds(items: HiddenSubtreeItem | HiddenSubtreeItem[]) {
+        const ids: (string | string[])[] = [];
+        if (Array.isArray(items)) {
+            for (const item of items) {
+                ids.push(getFlatIds(item));
+            }
+        } else {
+            if (items.children) {
+                for (const child of items.children) {
+                    ids.push(getFlatIds(child));
+                }
+            }
+            ids.push(items.id);
+        }
+        return ids.flat();
+    }
+
+    function getFlatIdsFromNote(note: BNote | null) {
+        if (!note) {
+            return [];
+        }
+
+        const ids: (string | string[])[] = [];
+
+        for (const subnote of note.getChildNotes()) {
+            ids.push(getFlatIdsFromNote(subnote));
+        }
+
+        ids.push(note.noteId);
+        return ids.flat();
+    }
+
+    const definitionHelpIds = new Set(getFlatIds(helpDefinition));
+    const realHelpIds = getFlatIdsFromNote(becca.getNote("_help"));
+
+    for (const realHelpId of realHelpIds) {
+        if (realHelpId === "_help") {
+            continue;
+        }
+
+        if (!definitionHelpIds.has(realHelpId)) {
+            becca.getNote(realHelpId)?.deleteNote();
+        }
+    }
+}