Leave the files in place, but move their contents elsewhere with a comment in the file to say where it went and why. This is especially useful where different parts of the file end up in different places. You should also put a comment in each new file indicating where the code originally came from and when it was moved to aid digging through code history.

After a period of time you may even get to remove the skeletons leaving just the cobwebs laying around in the (CVS) attic.

A related issue is: should one include check in history in the file or not. If history has been included it makes your boss's position less tenable becuase the history is in the file. On the other hand it tends to clutter the file with a lot of junk that inhibits searches (false hits in the check in comments are a real pain) and makes real code much harder to find.