Ah... the old poof!-all-my-mobis-became-pdfs
gnomes have been at it again? I thought we took care of them last time.
I suspect you may be looking at the disk's file contents though some kind of filter, and that all the mobis are still there (somewhere). Only because what you're describing seems pretty impossible, really. Mainly because A) the cd (if that's what you meant by "disk") is read-only, and B) I know of nothing that can perform the miraculous conversion of a read-only disk-full of mobi files to PDF (destroying the originals in the process) with a single button-click.
I bought the books because I have just bought my partner a Kindle touch for xmas and I wanted him to have some books to read straight away.
Then you still have considerable time to work this out.