This should solve your problem:
Put into PS3, format drive.
Do back up of this drive without initializing (raw uncompressed)
Do back up again (raw uncompressed)
Compared changes in HEX editor
Restore the ORIGINAL backup with all your information on it.
Place the unchanged changes onto the drive via HEX editor (don't forget to write the changes back to the drive)
Place drive back into PS3, restore databases via recovery menu.
Viola... I hope