I just added a bunch of community subscriptions via the webpage of my instance (lemmy.fmhy.ml) and they are visible there. But going to thunder they do not show up.
I logged out and back in, no change. I opened a different app I use, Voyager, there I see the communities as well. Is there a way to get them to update in thunder?
It is a known issue. What you are likely to find if you look is that 50 of your subs will load but they will be somewhat different each time. Sometimes one will load while others it wont. But you can still access it if you can find a post from it in the feed.