If these books are non-DRM, you should be able to fix at least the chapter links using Sigil (
http://code.google.com/p/sigil/ ). Links in epub files are coded as regular HTML links (since epub files are HTML), so it seems that you could easily get the links coded correctly and working again.
As far as bookmarks, I'm not sure. You could look at the help info on the Sigil website and see if it says anything about them.