"E:\filename.ai" is in an unknown format and cannot be opened"
OK. Now we're getting somewhere.
Without knowing more about the precise nature and cause of the "crash," we can only make guesses, and here's mine:
Basically, Katie, you're screwed.
My guess is that either the "crash" and/or your boss's subsequent handling of the D: drive (which might have been entirely proper) has caused data corruption on that drive.
If you have no backup for the files on the drive, and if those files are of critical importance, I would disconnect the drive immediately and get it to a data recovery specialist. The longer you have it connected, the more you reduce the chance of recovering data.
If the data are somewhat less than critical, you can try some basic recovery steps yourself. Start by making an image backup of the drive, then run chkdsk on it with the /r option. Rename any recovered files (with the .ai extension), and try opening them.
Finally, you might send the .ai files that won't open to a specialist who knows the Illustrator file format. He/she might be able to make some partial fixes that will, at least, enable you to open the files.
If you want, post up a few of the files on a server and post the link here. Some of the experts here might have a crack at it. (Put the files in a .zip archive first to protect them against further corruption during transfer.)