Fix Lit
If your notes links do not work you may have hit the incorrectly-mapped hyperlink bug
ConvertLIT has a bug which will cause references to files sharing a common filename prefix to all refer to one of the longer-named so-prefixed files. This bug is fixed in calibre, although you may need to use the command-line tool lit2oeb or lit2lrf with the --lit2oeb.
This most commonly shows up with footnotes because you'll have files like note1.html, note2.html, ..., note44.html. ConvertLIT internally has a list of filename IDs which are usually the filename without the extension (note1, ..., note44). To fix-up the link it searches through this list, but does so in a way which doesn't distinguish between a full match and an initial substring match. So if it's looking for 'note1' and it finds 'note14' first, then it'll link to 'note14.html' instead of 'note1.html'
Another way it shows up is if all notes are in the main body of the eBook (and not separate .htmls as above) and they point to either the table of contents or some other page not the main body of text.