Could you clarify a point for me. Is the disk a CD-ROM or similar? That is, a shiny silver (or possibly gold) disk about 12cm in diameter?
If so, and there were Mobipocket format books on that disk, then there still are Mobipocket format books on that disk.
Start again at the top level of the disk, and check the folders on the disk carefully. I suspect that there's one folder marked "Kindle" or "Mobipocket" and another marked "PDF", and you've just been looking in the wrong folder.
BTW, if the books on the disk aren't public domain books, you've almost certainly bought a disk of pirated ebooks.