diff --git a/src/services/code-index/processors/file-watcher.ts b/src/services/code-index/processors/file-watcher.ts
index a12752bea6..bff8d93a5f 100644
--- a/src/services/code-index/processors/file-watcher.ts
+++ b/src/services/code-index/processors/file-watcher.ts
@@ -203,6 +203,8 @@ export class FileWatcher implements IFileWatcher {
 				}
 			} catch (error) {
 				overallBatchError = error as Error
+				// Log the full, potentially multi-line, aggregated error message
+				console.error(`[FileWatcher] Failed to delete points for ${allPathsToClearFromDB.size} files:`, error)
 				for (const path of pathsToExplicitlyDelete) {
 					batchResults.push({ path, status: "error", error: error as Error })
 					processedCountInBatch++
diff --git a/src/services/code-index/processors/scanner.ts b/src/services/code-index/processors/scanner.ts
index 7b79a1c87d..234368ff79 100644
--- a/src/services/code-index/processors/scanner.ts
+++ b/src/services/code-index/processors/scanner.ts
@@ -309,11 +309,16 @@ export class DirectoryScanner implements IDirectoryScanner {
 							`[DirectoryScanner] Failed to delete points for ${uniqueFilePaths.length} files before upsert in workspace ${scanWorkspace}:`,
 							deleteError,
 						)
-						// Re-throw the error with workspace context
-						throw new Error(
-							`Failed to delete points for ${uniqueFilePaths.length} files. Workspace: ${scanWorkspace}. ${deleteError instanceof Error ? deleteError.message : String(deleteError)}`,
-							{ cause: deleteError },
-						)
+						// Log the error and call onError callback if it exists, but continue processing
+						if (onError) {
+							onError(
+								new Error(
+									`Failed to delete points for ${uniqueFilePaths.length} files. Workspace: ${scanWorkspace}. ${deleteError instanceof Error ? deleteError.message : String(deleteError)}`,
+									{ cause: deleteError },
+								),
+							)
+						}
+						// Continue processing instead of throwing
 					}
 				}
 				// --- End Deletion Step ---
diff --git a/src/services/code-index/vector-store/__tests__/qdrant-client.spec.ts b/src/services/code-index/vector-store/__tests__/qdrant-client.spec.ts
index bc4381edf2..dbafd0f639 100644
--- a/src/services/code-index/vector-store/__tests__/qdrant-client.spec.ts
+++ b/src/services/code-index/vector-store/__tests__/qdrant-client.spec.ts
@@ -9,10 +9,15 @@ import { DEFAULT_MAX_SEARCH_RESULTS, DEFAULT_SEARCH_MIN_SCORE } from "../../cons
 vitest.mock("@qdrant/js-client-rest")
 vitest.mock("crypto")
 vitest.mock("../../../../utils/path")
-vitest.mock("path", () => ({
-	...vitest.importActual("path"),
-	sep: "/",
-}))
+vitest.mock("path", async () => {
+	const actual = await vitest.importActual("path")
+	return {
+		...actual,
+		sep: "/",
+		resolve: vitest.fn((root, filePath) => `${root}/${filePath}`),
+		normalize: vitest.fn((path) => path),
+	}
+})
 
 const mockQdrantClientInstance = {
 	getCollection: vitest.fn(),
@@ -1291,4 +1296,155 @@ describe("QdrantVectorStore", () => {
 			expect(callArgs.score_threshold).toBe(DEFAULT_SEARCH_MIN_SCORE)
 		})
 	})
+	describe("deletePointsByMultipleFilePaths", () => {
+		const CHUNK_SIZE = 100 // As defined in the implementation
+		const MAX_RETRIES = 3 // As defined as MAX_BATCH_RETRIES in constants
+
+		beforeEach(() => {
+			// Mock timers to control retry logic in tests
+			vitest.useFakeTimers()
+			vitest.spyOn(console, "warn").mockImplementation(() => {})
+			vitest.spyOn(console, "error").mockImplementation(() => {})
+		})
+
+		afterEach(() => {
+			vitest.useRealTimers()
+		})
+
+		it("should handle an empty filePaths array gracefully", async () => {
+			await vectorStore.deletePointsByMultipleFilePaths([])
+			expect(mockQdrantClientInstance.delete).not.toHaveBeenCalled()
+		})
+
+		it("should delete a small batch of file paths in a single call", async () => {
+			const filePaths = ["src/file1.ts", "src/file2.ts"]
+			mockQdrantClientInstance.delete.mockResolvedValue({} as any)
+
+			await vectorStore.deletePointsByMultipleFilePaths(filePaths)
+
+			expect(mockQdrantClientInstance.delete).toHaveBeenCalledTimes(1)
+			const callArgs = mockQdrantClientInstance.delete.mock.calls[0][1]
+			expect(callArgs.filter.should).toHaveLength(2)
+		})
+
+		it("should split a large batch of file paths into multiple chunks", async () => {
+			const filePaths = Array.from({ length: 250 }, (_, i) => `src/file${i + 1}.ts`)
+			mockQdrantClientInstance.delete.mockResolvedValue({} as any)
+
+			await vectorStore.deletePointsByMultipleFilePaths(filePaths)
+
+			expect(mockQdrantClientInstance.delete).toHaveBeenCalledTimes(3) // 250 paths / 100 per chunk = 3 chunks
+			expect(mockQdrantClientInstance.delete.mock.calls[0][1].filter.should).toHaveLength(CHUNK_SIZE)
+			expect(mockQdrantClientInstance.delete.mock.calls[1][1].filter.should).toHaveLength(CHUNK_SIZE)
+			expect(mockQdrantClientInstance.delete.mock.calls[2][1].filter.should).toHaveLength(50)
+		})
+
+		it("should retry a failing chunk and succeed on the third attempt", async () => {
+			const filePaths = ["src/fail-then-succeed.ts"]
+			const deleteError = new Error("Qdrant unavailable")
+
+			mockQdrantClientInstance.delete
+				.mockRejectedValueOnce(deleteError)
+				.mockRejectedValueOnce(deleteError)
+				.mockResolvedValue({} as any)
+
+			const deletePromise = vectorStore.deletePointsByMultipleFilePaths(filePaths)
+
+			// Advance timers for each retry (INITIAL_RETRY_DELAY_MS = 500)
+			await vitest.advanceTimersByTimeAsync(500) // First retry delay (500ms)
+			await vitest.advanceTimersByTimeAsync(1000) // Second retry delay (500 * 2 = 1000ms)
+
+			await deletePromise
+
+			expect(mockQdrantClientInstance.delete).toHaveBeenCalledTimes(3)
+			expect(console.warn).toHaveBeenCalledTimes(2) // Warnings for the two failed attempts
+			expect(console.warn).toHaveBeenCalledWith(
+				expect.stringContaining("attempt 1/3. Retrying in 500ms..."),
+				deleteError.message,
+			)
+			expect(console.warn).toHaveBeenCalledWith(
+				expect.stringContaining("attempt 2/3. Retrying in 1000ms..."),
+				deleteError.message,
+			)
+		})
+
+		it("should throw an aggregated error if one chunk fails after all retries", async () => {
+			const filePaths = Array.from({ length: 150 }, (_, i) => `src/file${i + 1}.ts`)
+			const deleteError = new Error("Persistent failure")
+
+			// First chunk fails consistently, second chunk succeeds
+			mockQdrantClientInstance.delete
+				.mockRejectedValueOnce(deleteError)
+				.mockRejectedValueOnce(deleteError)
+				.mockRejectedValueOnce(deleteError)
+				.mockResolvedValue({} as any)
+
+			const deletePromise = vectorStore.deletePointsByMultipleFilePaths(filePaths)
+
+			// Advance timers for all retries of the first chunk (INITIAL_RETRY_DELAY_MS = 500)
+			await vitest.advanceTimersByTimeAsync(500) // First retry delay (500ms)
+			await vitest.advanceTimersByTimeAsync(1000) // Second retry delay (500 * 2 = 1000ms)
+			await vitest.advanceTimersByTimeAsync(2000) // Third retry delay (500 * 4 = 2000ms)
+
+			await expect(deletePromise).rejects.toThrow(
+				"Failed to delete 100 file paths across 1 chunks. Chunks failed: 1. First error: Persistent failure",
+			)
+
+			expect(mockQdrantClientInstance.delete).toHaveBeenCalledTimes(MAX_RETRIES + 1) // 3 retries for chunk 1 + 1 success for chunk 2
+			expect(console.error).toHaveBeenCalledTimes(1)
+			expect(console.error).toHaveBeenCalledWith(
+				`Failed to delete chunk 1 after ${MAX_RETRIES} attempts:`,
+				deleteError.message,
+			)
+
+			// Ensure all timers are run to completion
+			await vitest.runAllTimersAsync()
+		})
+
+		it("should throw an aggregated error if all chunks fail", async () => {
+			const filePaths = Array.from({ length: 220 }, (_, i) => `src/file${i + 1}.ts`)
+			const deleteError = new Error("Total cluster failure")
+
+			// All chunks fail
+			mockQdrantClientInstance.delete.mockRejectedValue(deleteError)
+
+			const deletePromise = vectorStore.deletePointsByMultipleFilePaths(filePaths)
+
+			// Advance timers for all retries of all chunks (INITIAL_RETRY_DELAY_MS = 500)
+			// Chunk 1 retries (3 attempts with exponential backoff)
+			await vitest.advanceTimersByTimeAsync(500) // First retry delay (500ms)
+			await vitest.advanceTimersByTimeAsync(1000) // Second retry delay (500 * 2 = 1000ms)
+			await vitest.advanceTimersByTimeAsync(2000) // Third retry delay (500 * 4 = 2000ms)
+			// Chunk 2 retries
+			await vitest.advanceTimersByTimeAsync(500) // First retry delay (500ms)
+			await vitest.advanceTimersByTimeAsync(1000) // Second retry delay (500 * 2 = 1000ms)
+			await vitest.advanceTimersByTimeAsync(2000) // Third retry delay (500 * 4 = 2000ms)
+			// Chunk 3 retries
+			await vitest.advanceTimersByTimeAsync(500) // First retry delay (500ms)
+			await vitest.advanceTimersByTimeAsync(1000) // Second retry delay (500 * 2 = 1000ms)
+			await vitest.advanceTimersByTimeAsync(2000) // Third retry delay (500 * 4 = 2000ms)
+
+			await expect(deletePromise).rejects.toThrow(
+				"Failed to delete 220 file paths across 3 chunks. Chunks failed: 1, 2, 3. First error: Total cluster failure",
+			)
+
+			expect(mockQdrantClientInstance.delete).toHaveBeenCalledTimes(MAX_RETRIES * 3) // 3 chunks * 3 retries each
+			expect(console.error).toHaveBeenCalledTimes(3)
+			expect(console.error).toHaveBeenCalledWith(
+				`Failed to delete chunk 1 after ${MAX_RETRIES} attempts:`,
+				deleteError.message,
+			)
+			expect(console.error).toHaveBeenCalledWith(
+				`Failed to delete chunk 2 after ${MAX_RETRIES} attempts:`,
+				deleteError.message,
+			)
+			expect(console.error).toHaveBeenCalledWith(
+				`Failed to delete chunk 3 after ${MAX_RETRIES} attempts:`,
+				deleteError.message,
+			)
+
+			// Ensure all timers are run to completion
+			await vitest.runAllTimersAsync()
+		})
+	})
 })
diff --git a/src/services/code-index/vector-store/qdrant-client.ts b/src/services/code-index/vector-store/qdrant-client.ts
index c8883959d5..2e45139360 100644
--- a/src/services/code-index/vector-store/qdrant-client.ts
+++ b/src/services/code-index/vector-store/qdrant-client.ts
@@ -4,7 +4,12 @@ import * as path from "path"
 import { getWorkspacePath } from "../../../utils/path"
 import { IVectorStore } from "../interfaces/vector-store"
 import { Payload, VectorStoreSearchResult } from "../interfaces"
-import { DEFAULT_MAX_SEARCH_RESULTS, DEFAULT_SEARCH_MIN_SCORE } from "../constants"
+import {
+	DEFAULT_MAX_SEARCH_RESULTS,
+	DEFAULT_SEARCH_MIN_SCORE,
+	MAX_BATCH_RETRIES,
+	INITIAL_RETRY_DELAY_MS,
+} from "../constants"
 import { t } from "../../../i18n"
 
 /**
@@ -333,29 +338,84 @@ export class QdrantVectorStore implements IVectorStore {
 			return
 		}
 
-		try {
-			const workspaceRoot = getWorkspacePath()
-			const normalizedPaths = filePaths.map((filePath) => {
-				const absolutePath = path.resolve(workspaceRoot, filePath)
-				return path.normalize(absolutePath)
-			})
+		const CHUNK_SIZE = 100
+		const workspaceRoot = getWorkspacePath()
+		const normalizedPaths = filePaths.map((filePath) => {
+			const absolutePath = path.resolve(workspaceRoot, filePath)
+			return path.normalize(absolutePath)
+		})
 
-			const filter = {
-				should: normalizedPaths.map((normalizedPath) => ({
-					key: "filePath",
-					match: {
-						value: normalizedPath,
-					},
-				})),
+		const failedChunks: { chunkIndex: number; paths: string[]; error: Error }[] = []
+
+		// Process paths in chunks
+		for (let i = 0; i < normalizedPaths.length; i += CHUNK_SIZE) {
+			const chunk = normalizedPaths.slice(i, i + CHUNK_SIZE)
+			const chunkIndex = Math.floor(i / CHUNK_SIZE)
+
+			// Retry logic with exponential backoff
+			let retryCount = 0
+			let lastError: Error | null = null
+
+			while (retryCount < MAX_BATCH_RETRIES) {
+				try {
+					const filter = {
+						should: chunk.map((normalizedPath) => ({
+							key: "filePath",
+							match: {
+								value: normalizedPath,
+							},
+						})),
+					}
+
+					await this.client.delete(this.collectionName, {
+						filter,
+						wait: true,
+					})
+
+					// Success - break out of retry loop
+					break
+				} catch (error) {
+					lastError = error instanceof Error ? error : new Error(String(error))
+					retryCount++
+
+					if (retryCount < MAX_BATCH_RETRIES) {
+						// Calculate exponential backoff delay
+						const delay = INITIAL_RETRY_DELAY_MS * Math.pow(2, retryCount - 1)
+						console.warn(
+							`Failed to delete chunk ${chunkIndex + 1} (paths ${i + 1}-${Math.min(i + CHUNK_SIZE, normalizedPaths.length)}), ` +
+								`attempt ${retryCount}/${MAX_BATCH_RETRIES}. Retrying in ${delay}ms...`,
+							lastError.message,
+						)
+
+						// Wait before retrying
+						await new Promise((resolve) => setTimeout(resolve, delay))
+					}
+				}
 			}
 
-			await this.client.delete(this.collectionName, {
-				filter,
-				wait: true,
-			})
-		} catch (error) {
-			console.error("Failed to delete points by file paths:", error)
-			throw error
+			// If all retries failed, log the error and continue to next chunk
+			if (retryCount === MAX_BATCH_RETRIES && lastError) {
+				console.error(
+					`Failed to delete chunk ${chunkIndex + 1} after ${MAX_BATCH_RETRIES} attempts:`,
+					lastError.message,
+				)
+				failedChunks.push({
+					chunkIndex,
+					paths: chunk,
+					error: lastError,
+				})
+			}
+		}
+
+		// If any chunks failed, throw an aggregated error
+		if (failedChunks.length > 0) {
+			const totalFailedPaths = failedChunks.reduce((sum, chunk) => sum + chunk.paths.length, 0)
+			const errorMessage =
+				`Failed to delete ${totalFailedPaths} file paths across ${failedChunks.length} chunks. ` +
+				`Chunks failed: ${failedChunks.map((c) => c.chunkIndex + 1).join(", ")}. ` +
+				`First error: ${failedChunks[0].error.message}`
+
+			throw new Error(errorMessage)
 		}
 	}