[godenderp]

I tried fixing the one for Grey's anatomy and refreshed it from the webinterface - ran another scan but still the episodes on disk are not added to the library.

Do you have the log for that?
Did you answer No to Refresh all episodes and Yes to Locally stored information found. Ignore and refresh from internet? That second question is a little bit quirky and many people answer No instead. 

I can probably grab the log for that, but I don't think I've seen the option "Locally stored information found" at all. FWIW I've navigated to the show on the web interface of the libreelec kodi instance and clicked on "more" and "refresh" "show only" and then get "Refreshing 'Grey's Anatomy' will remove it from the library then re-add it, so the ID may change. I'll attempt to reload this page with the new ID in a few seconds. Click 'YES' to confirm refresh".
It seems that's a different refresh than what you are talking about...