Thanks for the link and information Bookworm_Girl! I didn't backup the cache folder, since I thought... well, it's a cache-folder; who'd put something important there?
Sony really should rethink this whole concept of linking information over multiple places without a decent way to backup everything safely.
Well, just 300+ notes gone. The most dumb thing is that the information obviously somehow IS available in the annot files themselves, but cannot easily be converted... :-/