Back them up!!!
It is very important that you back up both the books and where possible the reader. I have had to reinstall all of my books (now well over 1000 titles) and their readers four times now, twice on new computers when the old laptop died. I have also had one publishing company (Embiid) go under on me, leaving me with 80 orphaned books. The biggest problem was with the readers, especaly the Mobipocket reader. That one made me redownload all of the books which had DRM.