Issues after Refactoring Source Model Name

I have three VDB's... all with the same three models in them with different combinations of visibility.

1. BQT (Source Model)
2. PART (Source Model)
3. VIRT (View Model)

If I re-factor the PART model name to PARTS I see the following:

1. My transformation query changed from SELECT * FROM PART.PARTS to SELECT * FROM PARTS.PARTSS
2. I can't consistently produce this one, but the third or first VDB has the new model name added but leaves the old one as well. So I end up with a PART and a PARTS.
3. When I click the synch button on PART in the vdb editor, I get an illegal argument exception.
4. When I try to remove PART, the VIRT model gets removed to because the Designer thinks there is still a dependency on PART by VIRT.