[dnanian]

I moved your message into its own thread, Art-Dude: it really didn't have anything to do with the other.

It sounds like you're using "Copy Newer" or "Copy Different" as your "During copy" method. These don't guarantee a bootable copy (because they never delete files from the source), but -- as you've said -- they also don't remove files from the destination, which can be desirable in some situations.

If you switch to Smart Update, it'll make the destination resemble the selections from the source again. This means any files deleted on the source (or not selected) will be removed.

You can't really startup from, and restore, a copy that's not Smart Update or Erase, then copy and expect it to be a "sensible" result because of the fact that no files have been deleted...