I'm pretty sure you've encountered a bug I was about to report however, I don't think it's a data loss bug, but rather a subtle but really problematic SAVING bug? Or maybe I've encountered a slightly different thing....
Let's say you're working with a VEP file called "Template A" and you choose to import instances from "Template Z"
The very next time you go to Save As, it DEFAULTS to calling your file "Template Z" and saving it in the SAME location as Template Z. Which means, if you aren't careful to NOTICE and CORRECT this, it will SAVE OVER "Template Z" with the NEW (potentially totally different except for whatever instances you just imported) from Z.
This is HIGHLY problematic, counter-intuitive, and should be fixed in my opinion RIGHT away. Just because I want to import an instance from Template Z (saved on drive/folder Z), doesn't mean I've now totally abandoned working on Template A (saved in drive/folder A).
Evan