I agree with tetonca in that it is the user's responsibility to keep their own backups or archived copies of mydata.tgz. If the system was to create a mydata.tgz~ backup of the backup, that would punish those who keep a rather large backup on a small partition as twice the disk space would be required.
And I get no error when I have an empty .filetool.lst and .xfiletool.lst and make a backup. So it appears you can empty your filetool files and make a backup if that is what you are wanting to do.