I only have the Emby config backup plugin generated last 10 dumps, which does not contain everything I believe, but if you can use the oldest one, I can upload it somewhere.
I was fiddling with debug logs, and also looked into the library.db file with SQLite:
I remember once /var/lib/emby was renamed /var/lib/emby-server. Then I created a symbolic link between the two, to continue to use Emby and everything was great. And now I have seen in the debug logs that the only options.xml that was parsed back with the /var/lib/emby folder was the Shorts library (only one, so correlates very well with the issue). And peeking into the DB (I made a dump and grepped a bit) I see many rows have this old folder in it (and not just this library, but others as well), so I presume that over time, this totally blew the DB away, and now is the time that you guys were not expecting this at all.
I think I will start over, the library for me is nothing sort of golden territory, so no big deal redoing everything from scratch. Not that I need to do it often, this is my biggest problem in this year using Emby
Thanks anyway, I think this does not require too much digging deep, as it might be a mess.