Developer and Support Tech
It sounds like he swapped the disk while Windows didn't flush it's caches yet, and file system transactions meant for disk A ended up being written to disk B. The presence of those folders could mean he ran Chkdsk. You can not undo this. You can only hope you can recover files.
Depending on what exactly happened iUndelete may do the trick. Just do a quick scan with the trial and see if the lost files show up. If so recover a few and see if they can be openen (you can do that with the trial version). If unsuccessful you can try iRecover.
WHATEVER YOU ATTEMPT THE DAMAGED DISK SHOULD NOT BE WRITTEN TO!