diff --git a/packages/tools/src/claude-memory.test.ts b/packages/tools/src/claude-memory.test.ts
index b5a9e636..3509541c 100644
--- a/packages/tools/src/claude-memory.test.ts
+++ b/packages/tools/src/claude-memory.test.ts
@@ -4,7 +4,9 @@ import { beforeEach, describe, expect, it, vi } from "vitest"
 // operations can be exercised deterministically without any network access.
 const documentsListMock = vi.fn()
 const documentsGetMock = vi.fn()
-const documentsDeleteBulkMock = vi.fn()
+const documentsDeleteBulkMock = vi
+	.fn()
+	.mockResolvedValue({ success: true, deletedCount: 1 })
 const addMock = vi.fn()
 
 vi.mock("supermemory", () => {
@@ -312,6 +314,13 @@ describe("ClaudeMemoryTool path traversal", () => {
 })
 
 describe("ClaudeMemoryTool path normalization collision resistance", () => {
+	beforeEach(() => {
+		documentsListMock.mockReset()
+		documentsGetMock.mockReset()
+		addMock.mockReset()
+		documentsDeleteBulkMock.mockReset()
+	})
+
 	it("produces distinct customIds for paths that previously collided", () => {
 		const tool = new ClaudeMemoryTool("test-api-key")
 		const paths = [
@@ -348,4 +357,93 @@ describe("ClaudeMemoryTool path normalization collision resistance", () => {
 		expect(result.success).toBe(true)
 		expect(result.content).toContain("legacy content")
 	})
+
+	it("cleans up legacy-customId document when str_replace updates the file", async () => {
+		mockDocuments([
+			{
+				id: "legacy-doc",
+				customId: "memories_notes_txt",
+				filePath: "/memories/notes.txt",
+				content: "legacy content hello",
+			},
+		])
+		documentsDeleteBulkMock.mockResolvedValue({
+			success: true,
+			deletedCount: 1,
+		})
+
+		const tool = new ClaudeMemoryTool("test-api-key")
+		const result = await tool.handleCommand({
+			command: "str_replace",
+			path: "/memories/notes.txt",
+			old_str: "hello",
+			new_str: "world",
+		})
+
+		expect(result.success).toBe(true)
+		expect(addMock).toHaveBeenCalledTimes(1)
+		expect(addMock.mock.calls[0]?.[0]?.customId).toBe("memories_s_notes_d_txt")
+		expect(documentsDeleteBulkMock).toHaveBeenCalledWith({
+			ids: ["legacy-doc"],
+		})
+	})
+
+	it("cleans up legacy-customId document when insert updates the file", async () => {
+		mockDocuments([
+			{
+				id: "legacy-doc",
+				customId: "memories_notes_txt",
+				filePath: "/memories/notes.txt",
+				content: "line1\nline2",
+			},
+		])
+		documentsDeleteBulkMock.mockResolvedValue({
+			success: true,
+			deletedCount: 1,
+		})
+
+		const tool = new ClaudeMemoryTool("test-api-key")
+		const result = await tool.handleCommand({
+			command: "insert",
+			path: "/memories/notes.txt",
+			insert_line: 2,
+			insert_text: "inserted line",
+		})
+
+		expect(result.success).toBe(true)
+		expect(addMock).toHaveBeenCalledTimes(1)
+		expect(addMock.mock.calls[0]?.[0]?.customId).toBe("memories_s_notes_d_txt")
+		expect(documentsDeleteBulkMock).toHaveBeenCalledWith({
+			ids: ["legacy-doc"],
+		})
+	})
+
+	it("cleans up legacy-customId document when create overwrites an existing file", async () => {
+		mockDocuments([
+			{
+				id: "legacy-doc",
+				customId: "memories_notes_txt",
+				filePath: "/memories/notes.txt",
+				content: "legacy content",
+			},
+		])
+		documentsDeleteBulkMock.mockResolvedValue({
+			success: true,
+			deletedCount: 1,
+		})
+
+		const tool = new ClaudeMemoryTool("test-api-key")
+		const result = await tool.handleCommand({
+			command: "create",
+			path: "/memories/notes.txt",
+			file_text: "brand new content",
+		})
+
+		expect(result.success).toBe(true)
+		expect(addMock).toHaveBeenCalledTimes(1)
+		expect(addMock.mock.calls[0]?.[0]?.customId).toBe("memories_s_notes_d_txt")
+		expect(documentsDeleteBulkMock).toHaveBeenCalledWith({
+			ids: ["legacy-doc"],
+		})
+	})
 })
diff --git a/packages/tools/src/claude-memory.ts b/packages/tools/src/claude-memory.ts
index 742d3144..e0b5b3de 100644
--- a/packages/tools/src/claude-memory.ts
+++ b/packages/tools/src/claude-memory.ts
@@ -41,6 +41,7 @@ type ClaudeFileMetadata = Record<string, string | number | boolean | string[]>
 
 interface ClaudeFileDocument {
 	documentId: string
+	customId?: string
 	content: string
 	metadata: ClaudeFileMetadata
 }
@@ -393,6 +394,8 @@ export class ClaudeMemoryTool {
 		fileText: string,
 	): Promise<MemoryResponse> {
 		try {
+			const existing = await this.getFileDocument(filePath)
+
 			const normalizedId = this.normalizePathToCustomId(filePath)
 
 			const _response = await this.client.add({
@@ -408,6 +411,17 @@ export class ClaudeMemoryTool {
 				},
 			})
 
+			// If an existing document was stored under a legacy customId, clean it up
+			// so the file path does not collide or become ambiguous with multiple documents.
+			if (
+				existing.success &&
+				existing.document &&
+				existing.document.customId &&
+				existing.document.customId !== normalizedId
+			) {
+				await deleteDocumentById(this.client, existing.document.documentId)
+			}
+
 			return {
 				success: true,
 				content: `File created: ${filePath}`,
@@ -466,6 +480,15 @@ export class ClaudeMemoryTool {
 				},
 			})
 
+			// If the modified file was stored under a legacy customId, clean up the legacy
+			// document to prevent path ambiguity.
+			if (
+				readResult.document.customId &&
+				readResult.document.customId !== normalizedId
+			) {
+				await deleteDocumentById(this.client, readResult.document.documentId)
+			}
+
 			return {
 				success: true,
 				content: `String replaced in file: ${filePath}`,
@@ -526,6 +549,15 @@ export class ClaudeMemoryTool {
 				},
 			})
 
+			// If the modified file was stored under a legacy customId, clean up the legacy
+			// document to prevent path ambiguity.
+			if (
+				readResult.document.customId &&
+				readResult.document.customId !== normalizedId
+			) {
+				await deleteDocumentById(this.client, readResult.document.documentId)
+			}
+
 			return {
 				success: true,
 				content: `Text inserted after line ${insertLine} in file: ${filePath}`,
@@ -756,7 +788,12 @@ export class ClaudeMemoryTool {
 
 			return {
 				success: true,
-				document: { documentId: candidate.id, content, metadata },
+				document: {
+					documentId: candidate.id,
+					customId: document.customId ?? candidate.customId,
+					content,
+					metadata,
+				},
 			}
 		} catch (error) {
 			return {