It seems that when objects are deleted from System, the corresponding data structures are not removed from Zync. It might be like that by design (to keep history of all updates), but it means that the DB becomes cluttered, and it may cause some inconsistencies.

We need to find a way to do either of those:

• trigger "database cleanup" on demand, something like we do backend storage rewrite (except that it also just makes sure to update the existing data, but probably will not remove stale records)
• maintain the DB clean, which means that we'd need to detect the situations when the object is deleted, and delete the records immediately (but that might be problematic, because the events might not reach zync in the right order)
• investigate what would be the consequences if we just clear the DB and let the stuff get recreated on the go - I'd say nothing too bad would happen, as System is source of truth, and in on-premises the DB storage is ephemeral anyway by default.