I was re-vaulting from one master to another. The job finished and I checked the source vault, it was empty.
I ran wContentVerify against the source and target, no problems reported.
I tried to delete the root folder of the source and Windchill told me it was still in use. I opened a ticket and the support engineer pointed me to Article - CS53958.
I deleted the orphaned fvitem records and I was able to delete the root folder. My initial thought was that there should be a WinRu to clean up orphaned records. Then I thought they are type of un-referenced file, so that should clean them up.
PTC says the records are not a problem and that is why there is an article.
I started looking at other tables like MasteredOnReplicaItem and StreamData. Same problem there.
Sometimes I find a relationship records where Object A or Object B was deleted, but the relation still points to it.
I used to admin a different PLM system and it had utilities for purifying the database. They would look for missing references and report them to the admin. The admin decides what to do about it. I think it helps to keep the database cleaned up. There types of discrepancies cause big problems with Windchill Bulk Migrator.
I suggest that PTC provide utilities ( not sql scripts ) to identify data inconsistencies and give the admin the visibility and opportunity to decide what to do about it. Maybe even make a recommendation. The other PLM system provided a report that could be easily converted to sql using search and replace.