diff --git a/src/stores/sync_config.js b/src/stores/sync_config.js
index 2ee3bba7d..009ccbce4 100644
--- a/src/stores/sync_config.js
+++ b/src/stores/sync_config.js
@@ -139,7 +139,7 @@ export const _getRecentData = (cache, live, isTest) => {
       result.stale = live
     } else {
       console.debug(
-        'Different timestamp, figuring out which one is more recent',
+        'Different timestamp or version, figuring out which one is more recent',
       )
       if (live._timestamp < cache._timestamp) {
         result.recent = cache
@@ -522,6 +522,7 @@ export const useSyncConfigStore = defineStore('sync_config', {
         const collection = new Set(get(this.prefsStorage, path))
         collection.delete(value)
         set(this.prefsStorage, path, [...collection])
+
         this.prefsStorage._journal = [
           ...this.prefsStorage._journal,
           {
@@ -535,8 +536,19 @@ export const useSyncConfigStore = defineStore('sync_config', {
       } else if (path.startsWith('objectCollection')) {
         const collection = new Set(get(this.prefsStorage, path + '.index'))
         collection.delete(_key)
+        set(this.prefsStorage, path + '.index', [...collection])
         const data = get(this.prefsStorage, path + '.data')
         delete data[_key]
+
+        this.prefsStorage._journal = [
+          ...this.prefsStorage._journal,
+          {
+            operation: 'removeFromCollection',
+            path,
+            args: [{ _key }],
+            timestamp: Date.now(),
+          },
+        ]
       }
     },
     reorderCollectionPreference({ path, value, movement }) {
@@ -579,14 +591,13 @@ export const useSyncConfigStore = defineStore('sync_config', {
       const live = userData.storage
       this.raw = live
       let cache = this.cache
-      if (cache && cache._user !== userData.fqn) {
+      if (cache?._user !== userData.fqn) {
         console.warn(
           'Cache belongs to another user! reinitializing local cache!',
         )
         cache = null
       }
-
-      cache = _doMigrations(cache, live)
+      console.log(cache, live)
 
       let { recent, stale, needUpload } = _getRecentData(cache, live)
 
@@ -604,6 +615,9 @@ export const useSyncConfigStore = defineStore('sync_config', {
         })
       }
 
+      recent = recent && _doMigrations(recent)
+      stale = stale && _doMigrations(stale)
+
       if (!needUpload && recent && stale) {
         console.debug('Checking if data needs merging...')
         // discarding timestamps and versions
diff --git a/test/unit/specs/modules/sync_config.spec.js b/test/unit/specs/stores/sync_config.spec.js
similarity index 96%
rename from test/unit/specs/modules/sync_config.spec.js
rename to test/unit/specs/stores/sync_config.spec.js
index 7b6008a67..abcddbeb1 100644
--- a/test/unit/specs/modules/sync_config.spec.js
+++ b/test/unit/specs/stores/sync_config.spec.js
@@ -16,7 +16,7 @@ import {
   VERSION,
 } from 'src/stores/sync_config.js'
 
-describe.skip('The SyncConfig module', () => {
+describe('The SyncConfig module', () => {
   beforeEach(() => {
     setActivePinia(createPinia())
   })
@@ -30,7 +30,7 @@ describe.skip('The SyncConfig module', () => {
 
       it('should initialize storage if none present', () => {
         const store = useSyncConfigStore()
-        store.setSyncConfig(store, user)
+        store.setSyncConfig({ ...user })
         expect(store.cache._version).to.eql(VERSION)
         expect(store.cache._timestamp).to.be.a('number')
         expect(store.cache.flagStorage).to.eql(defaultState.flagStorage)
@@ -95,7 +95,7 @@ describe.skip('The SyncConfig module', () => {
         expect(store.cache.flagStorage.updateCounter).to.eql(999)
       })
 
-      it('should remote version if local missing', () => {
+      it('should use remote version if local missing', () => {
         const store = useSyncConfigStore()
         store.setSyncConfig(store, user)
         expect(store.cache._version).to.eql(VERSION)
@@ -127,14 +127,26 @@ describe.skip('The SyncConfig module', () => {
           path: 'objectCollections.testing',
           value: { _key: 'a', foo: 1 },
         })
+        expect(store.prefsStorage.objectCollections.testing).to.eql({
+          data: { a: { _key: 'a', foo: 1 } },
+          index: ['a'],
+        })
         store.removeCollectionPreference({
           path: 'collections.testing',
           value: 2,
         })
+        store.removeCollectionPreference({
+          path: 'objectCollections.testing',
+          value: { _key: 'a' },
+        })
         store.updateCache({ username: 'test' })
         expect(store.prefsStorage.simple.testing).to.eql(2)
         expect(store.prefsStorage.collections.testing).to.eql([])
-        expect(store.prefsStorage._journal.length).to.eql(2)
+        expect(store.prefsStorage.objectCollections.testing).to.eql({
+          data: {},
+          index: [],
+        })
+        expect(store.prefsStorage._journal.length).to.eql(3)
         expect(store.prefsStorage._journal[0]).to.eql({
           path: 'simple.testing',
           operation: 'set',
@@ -152,7 +164,7 @@ describe.skip('The SyncConfig module', () => {
         expect(store.prefsStorage._journal[2]).to.eql({
           path: 'objectCollections.testing',
           operation: 'removeFromCollection',
-          args: [{ _key: 'a', foo: 1 }],
+          args: [{ _key: 'a' }],
           // should have A timestamp, we don't really care what it is
           timestamp: store.prefsStorage._journal[2].timestamp,
         })
@@ -179,7 +191,7 @@ describe.skip('The SyncConfig module', () => {
           data: { a: { _key: 'a', foo: 1 } },
           index: ['a'],
         })
-        expect(store.prefsStorage._journal.length).to.eql(3)
+        expect(store.prefsStorage._journal.length).to.eql(4)
       })
 
       it('should remove depth = 3 set/unset entries from journal', () => {