Hmm, was Sync enabled in the profile before you copied it over? That could explain how changes to a separate profile got copied back to the original. If that was the conduit for changes, make sure to disconnect that first. Next, changes to the current (synchronized) bookmarks shouldn't affect the backups. If you call up the Restore menu on your regular profile, can you pull up the previous day's backup? See: [[Restore bookmarks from backup or move them to another computer]]. Any luck so far? How old is the data in Old Firefox Data?