you will be glad you made a backup, you are going to need it.................
Sorry but it's standard practice that if a file or files are written over previous files, that the previous files are no longer viewable. It's not a 'fault' of any particular software program, rather human error.
If I today make an update of my site.com and upload it, my old site.com is written over and gone.
But just be glad that you had made a backup, even though it may need updating.