i haven't experienced this but i did have to reload my side loaded books twice. good thing i only have 18 or so loaded. one thing for sure is i don't use the kobo desktop app at all. i used it to get the upgrade and that's it.
i use ade, without my kobo plugged in, to download my books that i purchase.
after closing ade i open up calibre and load all of my books through that, even the ones i purchase.
seems a lot easier than using the other applications that seemed to cause my problems and i haven't experienced any major problems yet.