[dnanian]

It depends entirely on the "during copy" method you choose. Smart Update or Erase, then copy will delete them. Copy newer and Copy different will leave them on the drive, where they were. Of course, this makes things more difficult to restore, and doesn't guarantee a bootable backup.

My suggestion, in general, is to rotate "Smart Update" backups to cover this case. See the Introduction to the User's Guide for more.