1. I open an assembly that is comprised of both 1) read-only controlled files and 2) engineering uncontrolled files.

2. I do not select "Rebuild" assembly

3. I delete all read-only controlled parts from the assembly

4. I save the assembly

Now SolidWorks says: Hey! Listen! Remember all those parts you had open! Can I please save them again?

This is an infuriating bug. Please fix with the next service pack.