The gallery part of Zenphoto is entirely file system based and syncing the database with what is actually on the file system (not vice versa) is the core feature. This allows the simple upload via FTP to folders. This feature cannot be disabled.
The actutal image metadata (EXIF/IPTC) is by nature included in the image itself if Zenphoto reads it so it will re-read it as soon it can access the albums and images again.
Of course all data added manually (we don't call that meta data actually) and not embedded will be lost or overwritten by the meta data import (like titles or descriptions if set for example)
So the first "that user" (

) should do is perform frequent backups. There is an included plugin. If all albums and images are still thereafter repairing/resetting the messed up permissions all data could be restored.
I hope this helps a bit.