[EowynCarter]

Well, understanding what happened might help with finding a fix.
Sometimes even new hard drive can be defective.

What about the rest of the data on it? Is windows installed on that hard drive?
If that's indeed the hard drive, there should be other symptoms. What test did you ran?

I doubt calibre would break that many files at once. Did you do something particular? Do you use plug-ins?

Yup, what about the files in the calibre folder itself?

If zip archives got corrupted, I don't think it possible to get them back. Maybe some recovery program, or a company specialized in getting back lost hard drive data.