diff --git a/src/components/NoteManager/NoteManager.tsx b/src/components/NoteManager/NoteManager.tsx
index 8a643bd2..660411a8 100644
--- a/src/components/NoteManager/NoteManager.tsx
+++ b/src/components/NoteManager/NoteManager.tsx
@@ -1,7 +1,7 @@
 import { memo, useCallback, useContext, useEffect, useRef } from "react";
 import "./NoteManager.css";
 import type { ISynctexBlockId } from "@fluffylabs/links-metadata";
-import { cn } from "@fluffylabs/shared-ui";
+import { Alert, Button, cn } from "@fluffylabs/shared-ui";
 import { twMerge } from "tailwind-merge";
 import { useLatestCallback } from "../../hooks/useLatestCallback";
 import { type ILocationContext, LocationContext } from "../LocationProvider/LocationProvider";
@@ -12,6 +12,7 @@ import { type ISelectionContext, SelectionContext } from "../SelectionProvider/S
 import { InactiveNoteSkeleton } from "./components/InactiveNoteSkeleton";
 import { NewNote } from "./components/NewNote";
 import { NotesList } from "./components/NotesList";
+import { useFilteredNoteAlert } from "./hooks/useFilteredNoteAlert";
 import { useNoteManagerNotes } from "./useNoteManagerNotes";
 
 const DEFAULT_AUTHOR = "";
@@ -31,7 +32,7 @@ function Notes() {
   const {
     notesManagerNotes: notes,
     activeNotes,
-    latestHandleAddNote,
+    addNote,
     sectionTitlesLoaded,
     notesReady,
     deleteNote,
@@ -40,6 +41,7 @@ function Notes() {
   const { selectedBlocks, pageNumber, handleClearSelection } = useContext(SelectionContext) as ISelectionContext;
   const keepShowingNewNote = useRef<{ selectionEnd: ISynctexBlockId; selectionStart: ISynctexBlockId }>(undefined);
   const latestHandleClearSelection = useLatestCallback(handleClearSelection);
+  const { noteAlertVisibilityState, triggerFilteredNoteAlert, closeNoteAlert } = useFilteredNoteAlert();
 
   const memoizedHandleDeleteNote = useCallback(
     (note: IDecoratedNote) => {
@@ -53,9 +55,14 @@ function Notes() {
     (note: IDecoratedNote, newNote: IStorageNote) => {
       // NOTE(optimistic): intentional mutation for immediate UI feedback; be aware this bypasses immutability
       note.original.content = newNote.content;
-      updateNote(note, newNote);
+      note.original.labels = newNote.labels;
+      const { isVisible } = updateNote(note, newNote);
+      if (!isVisible) {
+        handleClearSelection();
+        triggerFilteredNoteAlert("visibleForUpdated");
+      }
     },
-    [updateNote],
+    [updateNote, handleClearSelection, triggerFilteredNoteAlert],
   );
 
   const handleNewNoteCancel = useCallback(() => {
@@ -84,13 +91,19 @@ function Notes() {
         labels,
       };
 
-      latestHandleAddNote.current(newNote);
+      const { isVisible } = addNote(newNote);
+
+      if (!isVisible) {
+        triggerFilteredNoteAlert("visibleForCreated");
+        handleClearSelection();
+      }
+
       keepShowingNewNote.current = {
         selectionStart: locationParams.selectionStart,
         selectionEnd: locationParams.selectionEnd,
       };
     },
-    [pageNumber, selectedBlocks, locationParams, latestHandleAddNote],
+    [pageNumber, selectedBlocks, locationParams, addNote, handleClearSelection, triggerFilteredNoteAlert],
   );
 
   const locationRef = useRef({ locationParams, setLocationParams });
@@ -133,44 +146,65 @@ function Notes() {
   }, [readyAndLoaded]);
 
   return (
-    <div className={cn("note-manager flex flex-col gap-2.5", !readyAndLoaded && "opacity-30 pointer-events-none")}>
-      {locationParams.selectionEnd &&
-        locationParams.selectionStart &&
-        pageNumber !== null &&
-        selectedBlocks.length > 0 &&
-        !isActiveNotes &&
-        (readyAndLoaded || areSelectionsEqual(locationParams, keepShowingNewNote.current)) && (
-          <NewNote
-            selectionStart={locationParams.selectionStart}
-            selectionEnd={locationParams.selectionEnd}
-            version={locationParams.version}
-            onCancel={handleNewNoteCancel}
-            onSave={handleAddNoteClick}
-          />
-        )}
-
-      {!readyAndLoaded && notes.length === 0 && (
-        <>
-          <InactiveNoteSkeleton />
-          <InactiveNoteSkeleton />
-          <InactiveNoteSkeleton />
-          <InactiveNoteSkeleton />
-        </>
+    <>
+      {noteAlertVisibilityState !== "hidden" && (
+        <Alert intent="warning">
+          <Alert.Title>
+            {noteAlertVisibilityState === "visibleForUpdated"
+              ? "Note hidden after update"
+              : "Note hidden by label filter"}
+          </Alert.Title>
+          <div className="flex gap-4">
+            <Alert.Text>
+              {noteAlertVisibilityState === "visibleForUpdated"
+                ? "Updated note doesn't match active labels."
+                : "Created note doesn't match active labels."}
+            </Alert.Text>
+            <Button variant="secondary" intent="warning" size="sm" className="self-end" onClick={closeNoteAlert}>
+              Close
+            </Button>
+          </div>
+        </Alert>
       )}
+      <div className={cn("note-manager flex flex-col gap-2.5", !readyAndLoaded && "opacity-30 pointer-events-none")}>
+        {locationParams.selectionEnd &&
+          locationParams.selectionStart &&
+          pageNumber !== null &&
+          selectedBlocks.length > 0 &&
+          !isActiveNotes &&
+          (readyAndLoaded || areSelectionsEqual(locationParams, keepShowingNewNote.current)) && (
+            <NewNote
+              selectionStart={locationParams.selectionStart}
+              selectionEnd={locationParams.selectionEnd}
+              version={locationParams.version}
+              onCancel={handleNewNoteCancel}
+              onSave={handleAddNoteClick}
+            />
+          )}
+
+        {!readyAndLoaded && notes.length === 0 && (
+          <>
+            <InactiveNoteSkeleton />
+            <InactiveNoteSkeleton />
+            <InactiveNoteSkeleton />
+            <InactiveNoteSkeleton />
+          </>
+        )}
 
-      {readyAndLoaded && notes.length === 0 && (
-        <div className="no-notes text-sidebar-foreground">No notes available</div>
-      )}
+        {readyAndLoaded && notes.length === 0 && (
+          <div className="no-notes text-sidebar-foreground">No notes available</div>
+        )}
 
-      {notes.length > 0 && (
-        <MemoizedNotesList
-          activeNotes={activeNotes}
-          notes={notes}
-          onEditNote={memoizedHandleUpdateNote}
-          onDeleteNote={memoizedHandleDeleteNote}
-          onSelectNote={memoizedHandleSelectNote}
-        />
-      )}
-    </div>
+        {notes.length > 0 && (
+          <MemoizedNotesList
+            activeNotes={activeNotes}
+            notes={notes}
+            onEditNote={memoizedHandleUpdateNote}
+            onDeleteNote={memoizedHandleDeleteNote}
+            onSelectNote={memoizedHandleSelectNote}
+          />
+        )}
+      </div>
+    </>
   );
 }
diff --git a/src/components/NoteManager/components/Note.tsx b/src/components/NoteManager/components/Note.tsx
index e9cfba98..20c6146a 100644
--- a/src/components/NoteManager/components/Note.tsx
+++ b/src/components/NoteManager/components/Note.tsx
@@ -22,7 +22,7 @@ type NoteProps = {
   note: IDecoratedNote;
   sectionTitles: { sectionTitle: string; subSectionTitle: string };
   active: boolean;
-  onEditNote: INotesContext["handleUpdateNote"];
+  onEditNote(noteToReplace: IDecoratedNote, newNote: IStorageNote): void;
   onDeleteNote: INotesContext["handleDeleteNote"];
   onSelectNote: (note: IDecoratedNote, opts: { type: "currentVersion" | "originalVersion" | "close" }) => void;
 };
diff --git a/src/components/NoteManager/components/NoteContext.tsx b/src/components/NoteManager/components/NoteContext.tsx
index 76807cdc..965b1e76 100644
--- a/src/components/NoteManager/components/NoteContext.tsx
+++ b/src/components/NoteManager/components/NoteContext.tsx
@@ -1,5 +1,4 @@
 import { createContext, useContext } from "react";
-import type { INotesContext } from "../../NotesProvider/NotesProvider";
 import type { IDecoratedNote } from "../../NotesProvider/types/DecoratedNote";
 import type { IStorageNote } from "../../NotesProvider/types/StorageNote";
 
@@ -13,7 +12,7 @@ export type ISingleNoteContext = {
   handleCancelClick: () => void;
   handleNoteLabelsChange: (labels: string[]) => void;
   noteDirty: IStorageNote;
-  onEditNote: INotesContext["handleUpdateNote"];
+  onEditNote: (noteToReplace: IDecoratedNote, newNote: IStorageNote) => void;
   isEditing: boolean;
   noteOriginalVersionShort: string | undefined;
   originalVersionLink: string | undefined;
diff --git a/src/components/NoteManager/hooks/useFilteredNoteAlert.ts b/src/components/NoteManager/hooks/useFilteredNoteAlert.ts
new file mode 100644
index 00000000..75fc1fa1
--- /dev/null
+++ b/src/components/NoteManager/hooks/useFilteredNoteAlert.ts
@@ -0,0 +1,37 @@
+import { useCallback, useEffect, useRef, useState } from "react";
+
+const FILTERED_NOTE_ALERT_MS = 6_000;
+
+export const useFilteredNoteAlert = () => {
+  const [noteAlertVisibilityState, setNoteAlertVisibilityState] = useState<
+    "hidden" | "visibleForCreated" | "visibleForUpdated"
+  >("hidden");
+  const alertTimeoutRef = useRef<number | null>(null);
+
+  const triggerFilteredNoteAlert = useCallback((type: "visibleForCreated" | "visibleForUpdated") => {
+    setNoteAlertVisibilityState(type);
+    if (alertTimeoutRef.current) {
+      window.clearTimeout(alertTimeoutRef.current);
+    }
+    alertTimeoutRef.current = window.setTimeout(() => {
+      setNoteAlertVisibilityState("hidden");
+    }, FILTERED_NOTE_ALERT_MS);
+  }, []);
+
+  useEffect(() => {
+    return () => {
+      if (alertTimeoutRef.current) {
+        window.clearTimeout(alertTimeoutRef.current);
+      }
+    };
+  }, []);
+
+  const closeNoteAlert = useCallback(() => {
+    setNoteAlertVisibilityState("hidden");
+    if (alertTimeoutRef.current) {
+      window.clearTimeout(alertTimeoutRef.current);
+    }
+  }, []);
+
+  return { noteAlertVisibilityState, triggerFilteredNoteAlert, closeNoteAlert };
+};
diff --git a/src/components/NoteManager/useNoteManagerNotes.ts b/src/components/NoteManager/useNoteManagerNotes.ts
index 71e9d685..a97d48bb 100644
--- a/src/components/NoteManager/useNoteManagerNotes.ts
+++ b/src/components/NoteManager/useNoteManagerNotes.ts
@@ -27,10 +27,19 @@ export const useNoteManagerNotes = () => {
   const latestDeleteNote = useLatestCallback(handleDeleteNote);
   const latestUpdateNote = useLatestCallback(handleUpdateNote);
 
+  const addNote = useCallback<INotesContext["handleAddNote"]>(
+    (noteToAdd) => {
+      const { isVisible } = latestHandleAddNote.current(noteToAdd);
+
+      return { isVisible };
+    },
+    [latestHandleAddNote],
+  );
+
   const updateNote = useCallback<INotesContext["handleUpdateNote"]>(
     (noteToReplace, newNote) => {
       metadataCacheByKey.current.delete(noteToReplace.key);
-      latestUpdateNote.current(noteToReplace, newNote);
+      return latestUpdateNote.current(noteToReplace, newNote);
     },
     [latestUpdateNote],
   );
@@ -106,7 +115,7 @@ export const useNoteManagerNotes = () => {
     sectionTitlesLoaded,
     notes,
     notesManagerNotes,
-    latestHandleAddNote,
+    addNote,
     deleteNote,
     updateNote,
   };
diff --git a/src/components/NotesProvider/NotesProvider.tsx b/src/components/NotesProvider/NotesProvider.tsx
index 8e8b2562..126de153 100644
--- a/src/components/NotesProvider/NotesProvider.tsx
+++ b/src/components/NotesProvider/NotesProvider.tsx
@@ -28,8 +28,8 @@ export interface INotesContext {
   canRedo: boolean;
   remoteSources: IRemoteSource[];
   handleSetRemoteSources(r: IRemoteSource, remove?: true): void;
-  handleAddNote(note: IStorageNote): void;
-  handleUpdateNote(noteToReplace: IDecoratedNote, newNote: IStorageNote): void;
+  handleAddNote(note: IStorageNote): { isVisible: boolean };
+  handleUpdateNote(noteToReplace: IDecoratedNote, newNote: IStorageNote): { isVisible: boolean };
   handleDeleteNote(note: IDecoratedNote): void;
   handleUndo(): void;
   handleRedo(): void;
@@ -105,7 +105,7 @@ export function NotesProvider({ children }: INotesProviderProps) {
 
   const allNotesReady = useMemo(() => localNotesReady && remoteNotesReady, [localNotesReady, remoteNotesReady]);
 
-  const { filteredNotes, labels, toggleLabel: handleToggleLabel } = useLabels(allNotes);
+  const { filteredNotes, labels, toggleLabel: handleToggleLabel, isVisibleByActiveLabelsLatest } = useLabels(allNotes);
 
   const handleSetRemoteSources = useCallback((newSource: IRemoteSource, remove?: true) => {
     setRemoteSources((prevRemoteSources) => {
@@ -148,27 +148,37 @@ export function NotesProvider({ children }: INotesProviderProps) {
     handleSetRemoteSources,
     handleToggleLabel,
     handleAddNote: useCallback(
-      (note) =>
+      (note) => {
+        const isVisible = isVisibleByActiveLabelsLatest.current(note);
+
         updateLocalNotes(localNotes, {
           ...localNotes,
           notes: [note, ...localNotes.notes],
-        }),
-      [localNotes, updateLocalNotes],
+        });
+
+        return { isVisible };
+      },
+      [localNotes, updateLocalNotes, isVisibleByActiveLabelsLatest],
     ),
     handleUpdateNote: useCallback(
       (noteToReplace, newNote) => {
         if (noteToReplace.source === NoteSource.Remote) {
           console.warn("Refusing to edit remote note.", noteToReplace);
-          return;
+          return { isVisible: true };
         }
+
+        const isVisible = isVisibleByActiveLabelsLatest.current(newNote);
+
         const updateIdx = localNotesDecorated.indexOf(noteToReplace);
         const newNotes = localNotes.notes.map((note, idx) => (updateIdx === idx ? newNote : note));
         updateLocalNotes(localNotes, {
           ...localNotes,
           notes: newNotes,
         });
+
+        return { isVisible };
       },
-      [localNotes, localNotesDecorated, updateLocalNotes],
+      [localNotes, localNotesDecorated, updateLocalNotes, isVisibleByActiveLabelsLatest],
     ),
     handleDeleteNote: useCallback(
       (noteToDelete) => {
diff --git a/src/components/NotesProvider/hooks/useLabels.ts b/src/components/NotesProvider/hooks/useLabels.ts
index 2b0efb0e..5abd4761 100644
--- a/src/components/NotesProvider/hooks/useLabels.ts
+++ b/src/components/NotesProvider/hooks/useLabels.ts
@@ -1,5 +1,6 @@
 import type { UnPrefixedLabel } from "@fluffylabs/links-metadata";
-import { useCallback, useEffect, useMemo, useState } from "react";
+import { type RefObject, useCallback, useEffect, useMemo, useState } from "react";
+import { useLatestCallback } from "../../../hooks/useLatestCallback";
 import { LABEL_LOCAL, LABEL_REMOTE } from "../consts/labels";
 import { type IDecoratedNote, NoteSource, isDecoratedNote } from "../types/DecoratedNote";
 import type { IStorageNote } from "../types/StorageNote";
@@ -119,6 +120,7 @@ export function useLabels(allNotes: IDecoratedNote[]): {
   filteredNotes: IDecoratedNote[];
   labels: ILabelTreeNode[];
   toggleLabel: (label: ILabelTreeNode) => void;
+  isVisibleByActiveLabelsLatest: RefObject<(note: IDecoratedNote | IStorageNote) => boolean>;
 } {
   const [storageLabels, setStorageLabels] = useState<IStorageLabel[]>([]);
   const [labels, setLabels] = useState<ILabelTreeNode[]>(initialEmptyArray as ILabelTreeNode[]);
@@ -226,12 +228,20 @@ export function useLabels(allNotes: IDecoratedNote[]): {
     });
   }, [allNotes, storageActivity]);
 
+  const activeLabels = useMemo(() => {
+    return labels.filter((label) => label.isActive).map((label) => label.prefixedLabel);
+  }, [labels]);
+
   // filter notes when labels are changing
   const filteredNotes = useMemo(() => {
-    const activeLabels = labels.filter((label) => label.isActive).map((label) => label.prefixedLabel);
     // filter out notes
     return getFilteredNotes(allNotes, activeLabels);
-  }, [allNotes, labels]);
+  }, [allNotes, activeLabels]);
+
+  const isVisibleByActiveLabelsLatest = useLatestCallback((note: IStorageNote | IDecoratedNote) => {
+    const filteringResult = getFilteredNotes([note], activeLabels);
+    return filteringResult.length > 0;
+  });
 
-  return { filteredNotes, labels, toggleLabel };
+  return { filteredNotes, labels, toggleLabel, isVisibleByActiveLabelsLatest };
 }