are the reading lists coming back or do we just start rebuilding them?

They're coming back however for me specifically, all my reading/finished mangas are put all put in already read.

And my want to read which had like 800 manga currently only have like 300.

Its been a few days since it updated to this stage so I'm not sure if it'll continue to update (and with more accuracy)...

My tags (and bookmarks) are still all there even when they weren't physically in any of my reading lists at the time. However now that all my mangas came back the personal notes that I made for them have all dissapeared.. idk if I'll ever get them back but I always used that as a way to know what chapter I left off on so ...

Yeah same, everything was put in my already read list. You should check there