Data loaded Account Territory Loader (ATL) records are not working properly. The ObjectTerritory2Association (OT2A) records are not deleted or created after the insert or upsert data load job.
The ATL records are not updated due to the large data loading batch size. If the batch size is larger than 20, a trigger copies the territory from the ATL fields and causes the OT2A records to not fire. This is because the Salesforce query limit is already reached.
Use a smaller batch size during the data loading. The optimal batch size is approximately 10-20.