We've had exactly this same experience twice in the past few months - our Registrar did a Restore / Merge and accidentally clicked to delete before merging. But, we do automated backups and have 10 or so old backups around just waiting for a need to restore them, so no problem, right? But wait - all the automated backups are gone!!!
The first time this happened I thought it was just coincidence that something had deleted the backups of the exact course we wanted to restore, but then it happened again. It seems that something about the "delete" function during a merge not only deletes content from the course itself but also DELETES ALL THE BACKUPS.
If that is intended, what a wacko design! Exactly when you need the backups that were so carefully created day after day, they are all deleted. This function needs to be changed to leave the backups alone.
Running 3.5, upgrading soon - has this been fixed in a newer version?