So far the most complete answer I have found is this : https://www.mangago.me/home/mangatopic/21080691/
(read the original post)
Tl;dr is : it may come back, or it may not, they're still working on it and it's a slow process.
Reply from the devs regarding the lists: https://www.mangago.me/thing/about/900021/

Guys ive been reading that a lot of people got back only mangas that they had tagged. This has happened to me too and they also all went to my i want to read list(its like 98 mangas out of 3k cause im dumb and I never tag stuff). Since a lot of conflicting answers have been circling around, like an alleged response to an email saying that there has been a loss of data during the restoration and only tagged mangas will come back, I just want to ask and understand if that's true. I'm not able to keep up with super long threads of answers and everyones saying something different, so If someone can confirm this version please let me know, cause I'll have to start rebuilding my lists manually