Okay, i'm not sure the way your software works. Most back up programs base their file selection on the "archive bit" which is set each time a file is changed or added. The backup software then looks for this and copies the changed files over the same backup file and resets the archive bit on the original file. It also adds any new files to the back up if they do not exist. As to files that have been deleted from the original locations, Most Software offers the option of retaininig these files for archaive pourposes or deleteing them from the back up drive.
HOW DOES YOUR SOFTWARE WORK?