Originally Posted by Raze
The saves may not be gone; running the game as administrator may simply have changed where the game is looking. Did you exit and run the game again not as administrator?
Normally each save is a separate subfolder in the '..\Divine Divinity\savegames' folder. Under Vista/7, depending on how the user accounts are set up, if you install the game to the Program Files path, Windows can create separate savegame folders for each user, and then map that folder to the game's savegame folder (so it will just see the saves for the relevant user).
C:\Users\ %account name% \AppData\Local\VirtualStore\Program Files\Divine Divinity\savegames
If running as administrator changes that behaviour, you may just have to copy/move the save files from the original location to what the game expects now.
If the saves did get deleted somehow, then for Vista/7/8, check if Windows made shadow copies of the saved games. You might be able to recover something with a program like Recuva, but the more you use the drive the saves are on the less likely that becomes.
Recover deleted files with Windows 7 shadow copies
Recover lost or deleted files