Save as text. Change the extension to ".html". Reimport to Calibre.
The problem is that PDB is not a single format, but a container which can hold data of any format. From the sound of it, you have a number of different formats, some of which convert correctly, and some of which don't.
If these were books you either bought or got free from Baen, you should be able to redownload them in modern formats.