I just did a new install on a server with PHP Version 5.2.13 and MySQL 5.0.45.
I added a few testalbums (no images) and made a backup. Then deleted the albums and tried to revert to the previous backup. This didn't work. Nothing changed.
To be sure I went on a bit and created a few new albums, made another backup, deleted those albums again and tried to revert to either one of the backups. No success so far .
Yes, that is expected behaviour. The backup,I supposed you refer to the backup utility on the backend overview, is for backup of the database (descriptions and such). If Zenphoto does not find the equivalent of an album on the filesystem it is deleted. Zenphoto creates albums filesystem based (as a long time user you should actually know that..;-).
Please read on our troubleshooting about doing such backups (move to another server or so the entry is called).