But do we still get notifications when a new chapter comes out? I follow thousands of them
I think you don't unless you follow it again, that's what happened the first time mangago fixed the first time. At least in the lists you've made, you get to see your favorite manga without the hassle of finding it again.
Fortunately, it's back to normal now. I didn't want to go through all that again. I already lost 2+k, the last time this happened. Back in January !! (Up until now, can't remember)
As long as the site is here, most of the mangas and manhwas can still be viewed. Just look for it again, make your own lists since it's not wiped out unlike the to be read, reading and already read options.