diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e50d26..d530dfa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,10 @@
 ### Fixes
 
 - GPU: respect explicit `QMD_LLAMA_GPU=metal|vulkan|cuda` backend overrides instead of always using auto GPU selection. #529
+- Fix: preserve original filename case in `handelize()`. The previous
+  `.toLowerCase()` call made indexed paths unreachable on case-sensitive
+  filesystems (Linux). `qmd update` automatically migrates legacy
+  lowercase paths without re-embedding.
 
 ## [2.1.0] - 2026-04-05
 
diff --git a/src/cli/qmd.ts b/src/cli/qmd.ts
index 9ba41ac..50ae764 100755
--- a/src/cli/qmd.ts
+++ b/src/cli/qmd.ts
@@ -45,6 +45,7 @@ import {
   insertContent,
   insertDocument,
   findActiveDocument,
+  findOrMigrateLegacyDocument,
   updateDocumentTitle,
   updateDocument,
   deactivateDocument,
@@ -1581,8 +1582,8 @@ async function indexFiles(pwd?: string, globPattern: string = DEFAULT_GLOB, coll
     const hash = await hashContent(content);
     const title = extractTitle(content, relativeFile);
 
-    // Check if document exists in this collection with this path
-    const existing = findActiveDocument(db, collectionName, path);
+    // Check if document exists (also migrates legacy lowercase paths)
+    const existing = findOrMigrateLegacyDocument(db, collectionName, path);
 
     if (existing) {
       if (existing.hash === hash) {
diff --git a/src/store.ts b/src/store.ts
index 098859c..16a55b7 100644
--- a/src/store.ts
+++ b/src/store.ts
@@ -1146,6 +1146,7 @@ export type Store = {
   insertContent: (hash: string, content: string, createdAt: string) => void;
   insertDocument: (collectionName: string, path: string, title: string, hash: string, createdAt: string, modifiedAt: string) => void;
   findActiveDocument: (collectionName: string, path: string) => { id: number; hash: string; title: string } | null;
+  findOrMigrateLegacyDocument: (collectionName: string, path: string) => { id: number; hash: string; title: string } | null;
   updateDocumentTitle: (documentId: number, title: string, modifiedAt: string) => void;
   updateDocument: (documentId: number, title: string, hash: string, modifiedAt: string) => void;
   deactivateDocument: (collectionName: string, path: string) => void;
@@ -1236,7 +1237,7 @@ export async function reindexCollection(
     const hash = await hashContent(content);
     const title = extractTitle(content, relativeFile);
 
-    const existing = findActiveDocument(db, collectionName, path);
+    const existing = findOrMigrateLegacyDocument(db, collectionName, path);
 
     if (existing) {
       if (existing.hash === hash) {
@@ -1659,6 +1660,7 @@ export function createStore(dbPath?: string): Store {
     insertContent: (hash: string, content: string, createdAt: string) => insertContent(db, hash, content, createdAt),
     insertDocument: (collectionName: string, path: string, title: string, hash: string, createdAt: string, modifiedAt: string) => insertDocument(db, collectionName, path, title, hash, createdAt, modifiedAt),
     findActiveDocument: (collectionName: string, path: string) => findActiveDocument(db, collectionName, path),
+    findOrMigrateLegacyDocument: (collectionName: string, path: string) => findOrMigrateLegacyDocument(db, collectionName, path),
     updateDocumentTitle: (documentId: number, title: string, modifiedAt: string) => updateDocumentTitle(db, documentId, title, modifiedAt),
     updateDocument: (documentId: number, title: string, hash: string, modifiedAt: string) => updateDocument(db, documentId, title, hash, modifiedAt),
     deactivateDocument: (collectionName: string, path: string) => deactivateDocument(db, collectionName, path),
@@ -1704,11 +1706,11 @@ export function getDocid(hash: string): string {
 /**
  * Handelize a filename to be more token-friendly.
  * - Convert triple underscore `___` to `/` (folder separator)
- * - Convert to lowercase
  * - Replace sequences of non-word chars (except /) with single dash
  * - Remove leading/trailing dashes from path segments
  * - Preserve folder structure (a/b/c/d.md stays structured)
  * - Preserve file extension
+ * - Preserve original case (important for case-sensitive filesystems)
  */
 /** Replace emoji/symbol codepoints with their hex representation (e.g. 🐘 → 1f418) */
 function emojiToHex(str: string): string {
@@ -1736,7 +1738,6 @@ export function handelize(path: string): string {
 
   const result = path
     .replace(/___/g, '/')       // Triple underscore becomes folder separator
-    .toLowerCase()
     .split('/')
     .map((segment, idx, arr) => {
       const isLastSegment = idx === arr.length - 1;
@@ -2114,6 +2115,57 @@ export function findActiveDocument(
   return row ?? null;
 }
 
+/**
+ * Find an active document, falling back to a legacy lowercase path.
+ * If found under the legacy path, renames it in-place and rebuilds the
+ * FTS entry. Embeddings are keyed by content hash, so the rename is
+ * safe — no re-embedding required.
+ *
+ * @internal Used by reindexCollection and indexFiles during qmd update.
+ * Returns null if the document does not exist under either path.
+ */
+export function findOrMigrateLegacyDocument(
+  db: Database,
+  collectionName: string,
+  path: string
+): { id: number; hash: string; title: string } | null {
+  const existing = findActiveDocument(db, collectionName, path);
+  if (existing) return existing;
+
+  const legacyPath = path.toLowerCase();
+  if (legacyPath === path) return null;
+
+  const legacy = findActiveDocument(db, collectionName, legacyPath);
+  if (!legacy) return null;
+
+  // Wrap rename + FTS rebuild in a transaction for atomicity.
+  const migrate = db.transaction(() => {
+    // Use OR IGNORE so a UNIQUE conflict (e.g. both "readme.md" and
+    // "README.md" already exist) is a no-op rather than crashing.
+    const result = db.prepare(
+      `UPDATE OR IGNORE documents SET path = ? WHERE id = ? AND active = 1`
+    ).run(path, legacy.id);
+
+    if (result.changes === 0) return false;
+
+    // FTS5 does not reliably update via the documents_au trigger's
+    // INSERT OR REPLACE. Manually rebuild the FTS entry.
+    db.prepare(`DELETE FROM documents_fts WHERE rowid = ?`).run(legacy.id);
+    db.prepare(`
+      INSERT INTO documents_fts(rowid, filepath, title, body)
+      SELECT id, collection || '/' || path, title,
+             (SELECT doc FROM content WHERE hash = documents.hash)
+      FROM documents WHERE id = ?
+    `).run(legacy.id);
+
+    return true;
+  });
+
+  if (!migrate()) return null;
+
+  return findActiveDocument(db, collectionName, path);
+}
+
 /**
  * Update the title and modified_at timestamp for a document.
  */
diff --git a/test/cli.test.ts b/test/cli.test.ts
index a95d8de..6b953f3 100644
--- a/test/cli.test.ts
+++ b/test/cli.test.ts
@@ -837,8 +837,8 @@ describe("CLI ls Command", () => {
   test("lists files in a collection", async () => {
     const { stdout, exitCode } = await runQmd(["ls", "fixtures"], { dbPath: localDbPath });
     expect(exitCode).toBe(0);
-    // handelize converts to lowercase
-    expect(stdout).toContain("qmd://fixtures/readme.md");
+    // handelize preserves original case
+    expect(stdout).toContain("qmd://fixtures/README.md");
     expect(stdout).toContain("qmd://fixtures/notes/meeting.md");
   });
 
@@ -847,8 +847,8 @@ describe("CLI ls Command", () => {
     expect(exitCode).toBe(0);
     expect(stdout).toContain("qmd://fixtures/notes/meeting.md");
     expect(stdout).toContain("qmd://fixtures/notes/ideas.md");
-    // Should not include files outside the prefix (handelize converts to lowercase)
-    expect(stdout).not.toContain("qmd://fixtures/readme.md");
+    // Should not include files outside the prefix (case preserved)
+    expect(stdout).not.toContain("qmd://fixtures/README.md");
   });
 
   test("lists files with virtual path", async () => {
diff --git a/test/store.helpers.unit.test.ts b/test/store.helpers.unit.test.ts
index 99af680..9adefc9 100644
--- a/test/store.helpers.unit.test.ts
+++ b/test/store.helpers.unit.test.ts
@@ -119,14 +119,14 @@ describe("cleanupOrphanedVectors", () => {
 // =============================================================================
 
 describe("handelize", () => {
-  test("converts to lowercase", () => {
-    expect(handelize("README.md")).toBe("readme.md");
-    expect(handelize("MyFile.MD")).toBe("myfile.md");
+  test("preserves original case", () => {
+    expect(handelize("README.md")).toBe("README.md");
+    expect(handelize("MyFile.MD")).toBe("MyFile.MD");
   });
 
   test("preserves folder structure", () => {
     expect(handelize("a/b/c/d.md")).toBe("a/b/c/d.md");
-    expect(handelize("docs/api/README.md")).toBe("docs/api/readme.md");
+    expect(handelize("docs/api/README.md")).toBe("docs/api/README.md");
   });
 
   test("replaces non-word characters with dash", () => {
@@ -156,7 +156,7 @@ describe("handelize", () => {
   test("handles complex real-world meeting notes", () => {
     const complexName = "Money Movement Licensing Review - 2025／11／19 10:25 EST - Notes by Gemini.md";
     const result = handelize(complexName);
-    expect(result).toBe("money-movement-licensing-review-2025-11-19-10-25-est-notes-by-gemini.md");
+    expect(result).toBe("Money-Movement-Licensing-Review-2025-11-19-10-25-EST-Notes-by-Gemini.md");
     expect(result).not.toContain(" ");
     expect(result).not.toContain("／");
     expect(result).not.toContain(":");
@@ -164,7 +164,7 @@ describe("handelize", () => {
 
   test("handles unicode characters", () => {
     expect(handelize("日本語.md")).toBe("日本語.md");
-    expect(handelize("Зоны и проекты.md")).toBe("зоны-и-проекты.md");
+    expect(handelize("Зоны и проекты.md")).toBe("Зоны-и-проекты.md");
     expect(handelize("café-notes.md")).toBe("café-notes.md");
     expect(handelize("naïve.md")).toBe("naïve.md");
     expect(handelize("日本語-notes.md")).toBe("日本語-notes.md");
@@ -186,13 +186,13 @@ describe("handelize", () => {
   test("handles dates and times in filenames", () => {
     expect(handelize("meeting-2025-01-15.md")).toBe("meeting-2025-01-15.md");
     expect(handelize("notes 2025/01/15.md")).toBe("notes-2025/01/15.md");
-    expect(handelize("call_10:30_AM.md")).toBe("call-10-30-am.md");
+    expect(handelize("call_10:30_AM.md")).toBe("call-10-30-AM.md");
   });
 
   test("handles special project naming patterns", () => {
-    expect(handelize("PROJECT_ABC_v2.0.md")).toBe("project-abc-v2-0.md");
-    expect(handelize("[WIP] Feature Request.md")).toBe("wip-feature-request.md");
-    expect(handelize("(DRAFT) Proposal v1.md")).toBe("draft-proposal-v1.md");
+    expect(handelize("PROJECT_ABC_v2.0.md")).toBe("PROJECT-ABC-v2-0.md");
+    expect(handelize("[WIP] Feature Request.md")).toBe("WIP-Feature-Request.md");
+    expect(handelize("(DRAFT) Proposal v1.md")).toBe("DRAFT-Proposal-v1.md");
   });
 
   test("handles symbol-only route filenames", () => {
diff --git a/test/store.test.ts b/test/store.test.ts
index 8b6400e..93bfb7d 100644
--- a/test/store.test.ts
+++ b/test/store.test.ts
@@ -3053,6 +3053,75 @@ describe("Content-Addressable Storage", () => {
 
     await cleanupTestDb(store);
   });
+
+  test("findOrMigrateLegacyDocument renames lowercase path to case-preserved", async () => {
+    const store = await createTestStore();
+    const collectionName = await createTestCollection();
+    const now = new Date().toISOString();
+
+    const content = "# My Skill";
+    const hash = await hashContent(content);
+    store.insertContent(hash, content, now);
+    // Simulate legacy index: path stored as lowercase
+    store.insertDocument(collectionName, "skills/skill.md", "My Skill", hash, now, now);
+
+    // Migration: look up case-preserved path, expect rename
+    const result = store.findOrMigrateLegacyDocument(collectionName, "skills/SKILL.md");
+    expect(result).not.toBeNull();
+    expect(result!.hash).toBe(hash);
+
+    // Old lowercase path should no longer be findable
+    expect(store.findActiveDocument(collectionName, "skills/skill.md")).toBeNull();
+    // New case-preserved path should be active
+    const migrated = store.findActiveDocument(collectionName, "skills/SKILL.md");
+    expect(migrated).not.toBeNull();
+    expect(migrated!.hash).toBe(hash);
+
+    // FTS should reflect the new path (documents_au trigger)
+    const ftsRow = store.db.prepare(
+      `SELECT filepath FROM documents_fts WHERE rowid = ?`
+    ).get(result!.id) as { filepath: string } | undefined;
+    expect(ftsRow).toBeDefined();
+    expect(ftsRow!.filepath).toContain("SKILL.md");
+
+    await cleanupTestDb(store);
+  });
+
+  test("findOrMigrateLegacyDocument returns null when path is already lowercase", async () => {
+    const store = await createTestStore();
+    const collectionName = await createTestCollection();
+
+    // No document exists at all
+    const result = store.findOrMigrateLegacyDocument(collectionName, "readme.md");
+    expect(result).toBeNull();
+
+    await cleanupTestDb(store);
+  });
+
+  test("findOrMigrateLegacyDocument returns existing doc when canonical path already present", async () => {
+    const store = await createTestStore();
+    const collectionName = await createTestCollection();
+    const now = new Date().toISOString();
+
+    const content = "# Content";
+    const hash = await hashContent(content);
+    store.insertContent(hash, content, now);
+    // Both lowercase and case-preserved paths exist (edge case from prior partial migration)
+    store.insertDocument(collectionName, "readme.md", "Readme", hash, now, now);
+    store.insertDocument(collectionName, "README.md", "README", hash, now, now);
+
+    // Should return the canonical-path document directly (fast path)
+    // The legacy "readme.md" row is untouched — no rename attempted.
+    const result = store.findOrMigrateLegacyDocument(collectionName, "README.md");
+    expect(result).not.toBeNull();
+    expect(result!.hash).toBe(hash);
+
+    // Both rows still exist (legacy row not migrated, not deactivated here)
+    expect(store.findActiveDocument(collectionName, "readme.md")).not.toBeNull();
+    expect(store.findActiveDocument(collectionName, "README.md")).not.toBeNull();
+
+    await cleanupTestDb(store);
+  });
 });
 
 // =============================================================================