What books is it removing (ie no longer available) when you sync?
Easiest thing to do is get calibre, import all your books into it, and then just get in habit of importing new purchases into it. Then you dont have to worry about any book being removed. Its a great program. You can use it simply as a backup, or you can learn its organizational features etc.. (For the latter, go up to the HD forum, look for the TAGS on the right hand side. Then look for "calibre"within the tags. compulsivereader has explored it a lot the last few months and explained how to get various features working.
Think of the "enhanced" books as apps that only work on tablets. Dont know of a way to back them up. But if you have one already, log onto your account from your pc. Once your in, theres a spot where you can view your content there too. Check and see if downloadable from there (will have a wierd name, numeric. Worth a try.) "PagePerfect"seem to be pdfs. Which "should be" downloadable as well (again, weird numeric name) But they might not be viewable on an eink device.
Does that help?
I don't use Calibre, I just keep a separate folder and copy newly downloaded books into that folder. I don't know if that's even necessary, but better safe than sorry IMO.