diff --git a/.changeset/funny-pianos-allow.md b/.changeset/funny-pianos-allow.md
new file mode 100644
index 000000000..3df90e3bc
--- /dev/null
+++ b/.changeset/funny-pianos-allow.md
@@ -0,0 +1,5 @@
+---
+'@powersync/service-core': patch
+---
+
+Fix "operation exceeded time limit" error
diff --git a/.changeset/green-books-shout.md b/.changeset/green-books-shout.md
new file mode 100644
index 000000000..1b2ef8139
--- /dev/null
+++ b/.changeset/green-books-shout.md
@@ -0,0 +1,5 @@
+---
+'@powersync/service-core': patch
+---
+
+Fix storageStats error in metrics endpoint when collections don't exist.
diff --git a/.changeset/short-bats-sin.md b/.changeset/short-bats-sin.md
deleted file mode 100644
index a4d78cd5a..000000000
--- a/.changeset/short-bats-sin.md
+++ /dev/null
@@ -1,5 +0,0 @@
----
-'@powersync/service-sync-rules': minor
----
-
-Warn when identifiers are automatically convererted to lower case.
diff --git a/.changeset/stupid-maps-buy.md b/.changeset/stupid-maps-buy.md
deleted file mode 100644
index 79edadd48..000000000
--- a/.changeset/stupid-maps-buy.md
+++ /dev/null
@@ -1,6 +0,0 @@
----
-'@powersync/service-core': patch
-'@powersync/service-image': patch
----
-
-Fix checksum cache edge case with compacting
diff --git a/.changeset/wet-gorillas-remember.md b/.changeset/wet-gorillas-remember.md
deleted file mode 100644
index d80afc7e1..000000000
--- a/.changeset/wet-gorillas-remember.md
+++ /dev/null
@@ -1,5 +0,0 @@
----
-'@powersync/service-sync-rules': minor
----
-
-Expand supported combinations of the IN operator
diff --git a/.changeset/young-rockets-behave.md b/.changeset/young-rockets-behave.md
deleted file mode 100644
index e58472781..000000000
--- a/.changeset/young-rockets-behave.md
+++ /dev/null
@@ -1,5 +0,0 @@
----
-'@powersync/service-core': patch
----
-
-Fix "JavaScript heap out of memory" on startup (slot health check)
diff --git a/packages/service-core/CHANGELOG.md b/packages/service-core/CHANGELOG.md
index 355a2301b..e76e019d4 100644
--- a/packages/service-core/CHANGELOG.md
+++ b/packages/service-core/CHANGELOG.md
@@ -1,5 +1,15 @@
 # @powersync/service-core
 
+## 0.8.5
+
+### Patch Changes
+
+- 1fd50a5: Fix checksum cache edge case with compacting
+- aa4eb0a: Fix "JavaScript heap out of memory" on startup (slot health check)
+- Updated dependencies [9e78ff1]
+- Updated dependencies [0e16938]
+  - @powersync/service-sync-rules@0.19.0
+
 ## 0.8.4
 
 ### Patch Changes
diff --git a/packages/service-core/package.json b/packages/service-core/package.json
index 9001441b9..b2fe5b340 100644
--- a/packages/service-core/package.json
+++ b/packages/service-core/package.json
@@ -5,7 +5,7 @@
   "publishConfig": {
     "access": "public"
   },
-  "version": "0.8.4",
+  "version": "0.8.5",
   "main": "dist/index.js",
   "license": "FSL-1.1-Apache-2.0",
   "type": "module",
diff --git a/packages/service-core/src/db/mongo.ts b/packages/service-core/src/db/mongo.ts
index 33d6d5b86..f687705bd 100644
--- a/packages/service-core/src/db/mongo.ts
+++ b/packages/service-core/src/db/mongo.ts
@@ -23,6 +23,13 @@ export const MONGO_SOCKET_TIMEOUT_MS = 60_000;
  */
 export const MONGO_OPERATION_TIMEOUT_MS = 30_000;
 
+/**
+ * Same as above, but specifically for clear operations.
+ *
+ * These are retried when reaching the timeout.
+ */
+export const MONGO_CLEAR_OPERATION_TIMEOUT_MS = 5_000;
+
 export function createMongoClient(config: configFile.PowerSyncConfig['storage']) {
   const normalized = normalizeMongoConfig(config);
   return new mongo.MongoClient(normalized.uri, {
diff --git a/packages/service-core/src/storage/BucketStorage.ts b/packages/service-core/src/storage/BucketStorage.ts
index 9c12e805c..84165fb7c 100644
--- a/packages/service-core/src/storage/BucketStorage.ts
+++ b/packages/service-core/src/storage/BucketStorage.ts
@@ -265,8 +265,6 @@ export interface SyncRulesBucketStorage extends DisposableObserverClient<SyncRul
    */
   clear(): Promise<void>;
 
-  setSnapshotDone(lsn: string): Promise<void>;
-
   autoActivate(): Promise<void>;
 
   /**
diff --git a/packages/service-core/src/storage/MongoBucketStorage.ts b/packages/service-core/src/storage/MongoBucketStorage.ts
index c0254da71..9da62758c 100644
--- a/packages/service-core/src/storage/MongoBucketStorage.ts
+++ b/packages/service-core/src/storage/MongoBucketStorage.ts
@@ -331,39 +331,56 @@ export class MongoBucketStorage
   }
 
   async getStorageMetrics(): Promise<StorageMetrics> {
+    const ignoreNotExiting = (e: unknown) => {
+      if (e instanceof mongo.MongoServerError && e.codeName == 'NamespaceNotFound') {
+        // Collection doesn't exist - return 0
+        return [{ storageStats: { size: 0 } }];
+      } else {
+        return Promise.reject(e);
+      }
+    };
+
+    const active_sync_rules = await this.getActiveSyncRules({ defaultSchema: 'public' });
+    if (active_sync_rules == null) {
+      return {
+        operations_size_bytes: 0,
+        parameters_size_bytes: 0,
+        replication_size_bytes: 0
+      };
+    }
     const operations_aggregate = await this.db.bucket_data
 
       .aggregate([
         {
           $collStats: {
-            storageStats: {},
-            count: {}
+            storageStats: {}
           }
         }
       ])
-      .toArray();
+      .toArray()
+      .catch(ignoreNotExiting);
 
     const parameters_aggregate = await this.db.bucket_parameters
       .aggregate([
         {
           $collStats: {
-            storageStats: {},
-            count: {}
+            storageStats: {}
           }
         }
       ])
-      .toArray();
+      .toArray()
+      .catch(ignoreNotExiting);
 
     const replication_aggregate = await this.db.current_data
       .aggregate([
         {
           $collStats: {
-            storageStats: {},
-            count: {}
+            storageStats: {}
           }
         }
       ])
-      .toArray();
+      .toArray()
+      .catch(ignoreNotExiting);
 
     return {
       operations_size_bytes: operations_aggregate[0].storageStats.size,
diff --git a/packages/service-core/src/storage/mongo/MongoSyncBucketStorage.ts b/packages/service-core/src/storage/mongo/MongoSyncBucketStorage.ts
index 71ab4a531..e4b57788e 100644
--- a/packages/service-core/src/storage/mongo/MongoSyncBucketStorage.ts
+++ b/packages/service-core/src/storage/mongo/MongoSyncBucketStorage.ts
@@ -31,6 +31,8 @@ import { BucketDataDocument, BucketDataKey, SourceKey, SyncRuleState } from './m
 import { MongoBucketBatch } from './MongoBucketBatch.js';
 import { MongoCompactor } from './MongoCompactor.js';
 import { BSON_DESERIALIZE_OPTIONS, idPrefixFilter, mapOpEntry, readSingleBatch, serializeLookup } from './util.js';
+import { logger } from '@powersync/lib-services-framework';
+import * as timers from 'timers/promises';
 
 export class MongoSyncBucketStorage
   extends DisposableObserver<SyncRulesBucketStorageListener>
@@ -459,10 +461,28 @@ export class MongoSyncBucketStorage
   }
 
   async clear(): Promise<void> {
+    while (true) {
+      try {
+        await this.clearIteration();
+        return;
+      } catch (e: unknown) {
+        if (e instanceof mongo.MongoServerError && e.codeName == 'MaxTimeMSExpired') {
+          logger.info(
+            `Clearing took longer than ${db.mongo.MONGO_CLEAR_OPERATION_TIMEOUT_MS}ms, waiting and triggering another iteration.`
+          );
+          await timers.setTimeout(db.mongo.MONGO_CLEAR_OPERATION_TIMEOUT_MS / 5);
+          continue;
+        } else {
+          throw e;
+        }
+      }
+    }
+  }
+
+  private async clearIteration(): Promise<void> {
     // Individual operations here may time out with the maxTimeMS option.
     // It is expected to still make progress, and continue on the next try.
 
-    // TODO: Transactional?
     await this.db.sync_rules.updateOne(
       {
         _id: this.group_id
@@ -476,48 +496,33 @@ export class MongoSyncBucketStorage
           no_checkpoint_before: null
         }
       },
-      { maxTimeMS: db.mongo.MONGO_OPERATION_TIMEOUT_MS }
+      { maxTimeMS: db.mongo.MONGO_CLEAR_OPERATION_TIMEOUT_MS }
     );
     await this.db.bucket_data.deleteMany(
       {
         _id: idPrefixFilter<BucketDataKey>({ g: this.group_id }, ['b', 'o'])
       },
-      { maxTimeMS: db.mongo.MONGO_OPERATION_TIMEOUT_MS }
+      { maxTimeMS: db.mongo.MONGO_CLEAR_OPERATION_TIMEOUT_MS }
     );
     await this.db.bucket_parameters.deleteMany(
       {
         key: idPrefixFilter<SourceKey>({ g: this.group_id }, ['t', 'k'])
       },
-      { maxTimeMS: db.mongo.MONGO_OPERATION_TIMEOUT_MS }
+      { maxTimeMS: db.mongo.MONGO_CLEAR_OPERATION_TIMEOUT_MS }
     );
 
     await this.db.current_data.deleteMany(
       {
         _id: idPrefixFilter<SourceKey>({ g: this.group_id }, ['t', 'k'])
       },
-      { maxTimeMS: db.mongo.MONGO_OPERATION_TIMEOUT_MS }
+      { maxTimeMS: db.mongo.MONGO_CLEAR_OPERATION_TIMEOUT_MS }
     );
 
     await this.db.source_tables.deleteMany(
       {
         group_id: this.group_id
       },
-      { maxTimeMS: db.mongo.MONGO_OPERATION_TIMEOUT_MS }
-    );
-  }
-
-  async setSnapshotDone(lsn: string): Promise<void> {
-    await this.db.sync_rules.updateOne(
-      {
-        _id: this.group_id
-      },
-      {
-        $set: {
-          snapshot_done: true,
-          persisted_lsn: lsn,
-          last_checkpoint_ts: new Date()
-        }
-      }
+      { maxTimeMS: db.mongo.MONGO_CLEAR_OPERATION_TIMEOUT_MS }
     );
   }
 
diff --git a/packages/service-core/src/storage/mongo/db.ts b/packages/service-core/src/storage/mongo/db.ts
index dddfdf918..99bad0948 100644
--- a/packages/service-core/src/storage/mongo/db.ts
+++ b/packages/service-core/src/storage/mongo/db.ts
@@ -62,6 +62,9 @@ export class PowerSyncMongo {
     this.locks = this.db.collection('locks');
   }
 
+  /**
+   * Clear all collections.
+   */
   async clear() {
     await this.current_data.deleteMany({});
     await this.bucket_data.deleteMany({});
@@ -73,4 +76,13 @@ export class PowerSyncMongo {
     await this.instance.deleteOne({});
     await this.locks.deleteMany({});
   }
+
+  /**
+   * Drop the entire database.
+   *
+   * Primarily for tests.
+   */
+  async drop() {
+    await this.db.dropDatabase();
+  }
 }
diff --git a/packages/service-core/test/src/data_storage.test.ts b/packages/service-core/test/src/data_storage.test.ts
index 8eceacf40..05885b704 100644
--- a/packages/service-core/test/src/data_storage.test.ts
+++ b/packages/service-core/test/src/data_storage.test.ts
@@ -1438,4 +1438,26 @@ bucket_definitions:
     expect(errorCaught).true;
     expect(isDisposed).true;
   });
+
+  test('empty storage metrics', async () => {
+    const f = await factory({ dropAll: true });
+
+    const metrics = await f.getStorageMetrics();
+    expect(metrics).toEqual({
+      operations_size_bytes: 0,
+      parameters_size_bytes: 0,
+      replication_size_bytes: 0
+    });
+
+    const r = await f.configureSyncRules('bucket_definitions: {}');
+    const storage = f.getInstance(r.persisted_sync_rules!);
+    await storage.autoActivate();
+
+    const metrics2 = await f.getStorageMetrics();
+    expect(metrics2).toEqual({
+      operations_size_bytes: 0,
+      parameters_size_bytes: 0,
+      replication_size_bytes: 0
+    });
+  });
 }
diff --git a/packages/service-core/test/src/sync.test.ts b/packages/service-core/test/src/sync.test.ts
index f1c4c7272..606647038 100644
--- a/packages/service-core/test/src/sync.test.ts
+++ b/packages/service-core/test/src/sync.test.ts
@@ -5,15 +5,7 @@ import { JSONBig } from '@powersync/service-jsonbig';
 import { RequestParameters } from '@powersync/service-sync-rules';
 import * as timers from 'timers/promises';
 import { describe, expect, test } from 'vitest';
-import {
-  BATCH_OPTIONS,
-  makeTestTable,
-  MONGO_STORAGE_FACTORY,
-  PARSE_OPTIONS,
-  StorageFactory,
-  ZERO_LSN
-} from './util.js';
-import { ParseSyncRulesOptions, StartBatchOptions } from '@/storage/BucketStorage.js';
+import { BATCH_OPTIONS, makeTestTable, MONGO_STORAGE_FACTORY, PARSE_OPTIONS, StorageFactory } from './util.js';
 
 describe('sync - mongodb', function () {
   defineTests(MONGO_STORAGE_FACTORY);
@@ -38,8 +30,7 @@ function defineTests(factory: StorageFactory) {
       content: BASIC_SYNC_RULES
     });
 
-    const storage = await f.getInstance(syncRules);
-    await storage.setSnapshotDone(ZERO_LSN);
+    const storage = f.getInstance(syncRules);
     await storage.autoActivate();
 
     const result = await storage.startBatch(BATCH_OPTIONS, async (batch) => {
@@ -91,7 +82,6 @@ function defineTests(factory: StorageFactory) {
     });
 
     const storage = await f.getInstance(syncRules);
-    await storage.setSnapshotDone(ZERO_LSN);
     await storage.autoActivate();
 
     const result = await storage.startBatch(BATCH_OPTIONS, async (batch) => {
@@ -136,7 +126,6 @@ function defineTests(factory: StorageFactory) {
     });
 
     const storage = await f.getInstance(syncRules);
-    await storage.setSnapshotDone(ZERO_LSN);
     await storage.autoActivate();
 
     const stream = streamResponse({
@@ -164,7 +153,6 @@ function defineTests(factory: StorageFactory) {
     });
 
     const storage = await f.getInstance(syncRules);
-    await storage.setSnapshotDone(ZERO_LSN);
     await storage.autoActivate();
 
     const stream = streamResponse({
@@ -226,7 +214,6 @@ function defineTests(factory: StorageFactory) {
     });
 
     const storage = await f.getInstance(syncRules);
-    await storage.setSnapshotDone(ZERO_LSN);
     await storage.autoActivate();
 
     const exp = Date.now() / 1000 + 0.1;
@@ -265,7 +252,6 @@ function defineTests(factory: StorageFactory) {
     });
 
     const storage = await f.getInstance(syncRules);
-    await storage.setSnapshotDone(ZERO_LSN);
     await storage.autoActivate();
 
     await storage.startBatch(BATCH_OPTIONS, async (batch) => {
diff --git a/packages/service-core/test/src/util.ts b/packages/service-core/test/src/util.ts
index cd8c06f2c..98cd613e2 100644
--- a/packages/service-core/test/src/util.ts
+++ b/packages/service-core/test/src/util.ts
@@ -24,11 +24,22 @@ await Metrics.initialise({
 });
 Metrics.getInstance().resetCounters();
 
-export type StorageFactory = () => Promise<BucketStorageFactory>;
+export interface StorageOptions {
+  /**
+   * By default, collections are only cleared/
+   * Setting this to true will drop the collections completely.
+   */
+  dropAll?: boolean;
+}
+export type StorageFactory = (options?: StorageOptions) => Promise<BucketStorageFactory>;
 
-export const MONGO_STORAGE_FACTORY: StorageFactory = async () => {
+export const MONGO_STORAGE_FACTORY: StorageFactory = async (options?: StorageOptions) => {
   const db = await connectMongo();
-  await db.clear();
+  if (options?.dropAll) {
+    await db.drop();
+  } else {
+    await db.clear();
+  }
   return new MongoBucketStorage(db, { slot_name_prefix: 'test_' });
 };
 
diff --git a/packages/sync-rules/CHANGELOG.md b/packages/sync-rules/CHANGELOG.md
index 8045fd193..099bf11db 100644
--- a/packages/sync-rules/CHANGELOG.md
+++ b/packages/sync-rules/CHANGELOG.md
@@ -1,5 +1,12 @@
 # @powersync/service-sync-rules
 
+## 0.19.0
+
+### Minor Changes
+
+- 9e78ff1: Warn when identifiers are automatically convererted to lower case.
+- 0e16938: Expand supported combinations of the IN operator
+
 ## 0.18.3
 
 ### Patch Changes
diff --git a/packages/sync-rules/package.json b/packages/sync-rules/package.json
index ffe53c975..bb942b1e8 100644
--- a/packages/sync-rules/package.json
+++ b/packages/sync-rules/package.json
@@ -1,7 +1,7 @@
 {
   "name": "@powersync/service-sync-rules",
   "repository": "https://github.com/powersync-ja/powersync-service",
-  "version": "0.18.3",
+  "version": "0.19.0",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "license": "FSL-1.1-Apache-2.0",
diff --git a/service/CHANGELOG.md b/service/CHANGELOG.md
index 0dc13b29b..6c12e7529 100644
--- a/service/CHANGELOG.md
+++ b/service/CHANGELOG.md
@@ -1,5 +1,17 @@
 # @powersync/service-image
 
+## 0.5.5
+
+### Patch Changes
+
+- 1fd50a5: Fix checksum cache edge case with compacting
+- Updated dependencies [9e78ff1]
+- Updated dependencies [1fd50a5]
+- Updated dependencies [0e16938]
+- Updated dependencies [aa4eb0a]
+  - @powersync/service-sync-rules@0.19.0
+  - @powersync/service-core@0.8.5
+
 ## 0.5.4
 
 ### Patch Changes
diff --git a/service/package.json b/service/package.json
index 3a3d6652e..0e2f96478 100644
--- a/service/package.json
+++ b/service/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@powersync/service-image",
-  "version": "0.5.4",
+  "version": "0.5.5",
   "private": true,
   "license": "FSL-1.1-Apache-2.0",
   "type": "module",
diff --git a/test-client/CHANGELOG.md b/test-client/CHANGELOG.md
index e901b1e55..9c90f775c 100644
--- a/test-client/CHANGELOG.md
+++ b/test-client/CHANGELOG.md
@@ -1,5 +1,13 @@
 # test-client
 
+## 0.1.7
+
+### Patch Changes
+
+- Updated dependencies [1fd50a5]
+- Updated dependencies [aa4eb0a]
+  - @powersync/service-core@0.8.5
+
 ## 0.1.6
 
 ### Patch Changes
diff --git a/test-client/package.json b/test-client/package.json
index 075a7bb32..5e311c708 100644
--- a/test-client/package.json
+++ b/test-client/package.json
@@ -2,7 +2,7 @@
   "name": "test-client",
   "repository": "https://github.com/powersync-ja/powersync-service",
   "private": true,
-  "version": "0.1.6",
+  "version": "0.1.7",
   "main": "dist/index.js",
   "bin": "dist/bin.js",
   "license": "Apache-2.0",