Virtual Copies, Stacks and Collections are all lost when you remove images from the database. I hope my advice didn't really screw things up for you. When I did this, I had only 9 images afffected, and no Virtual Copies or Stacks. The Collections were easy enough to update.
I should have recommended you Export as Catalog first, then remove the files, then re-import from the temporary catalog. You'd retain everything that way. Using temporary working databases can really be a time saver.
Well. I wish I had known about Virtual copies - I did loose one that had a couple of hours processing and spotting in it - thankfully I had a TIFF conversion, so its not a major issue.
Regardless - I am happy that your suggestion solved the problem.