Well I tried to re-add the books and although I had the option checked to merge the files automatically it did not link the new file types into the database. So, I deleted all the books and then re-added them. One good thing, it imported all the books and I was able to retain my original dates, I assume this is because this data is saved in the opf files. One bad thing, I lost all my covers, but this is not a major loss, I will fix them as I go along.
Thanks to all for your assistance.
Now off to setup my backup program to backup the directories so I do not need to go through this again. I did see some posts about dropbox, but I am a little hesitant about putting my books on the web so I need to research that before thinking about using something like that.