I believe there's a bug when a moderator from a remote instance edits a community, that stops it showing up in search and makes it only accessible via a link like https://feddit.de/c/japanesemusic@feddit.de. So that's probably what happened to this one. More info.
As for the other stuff, Beehaw is defederated from sh.itjust.works so makes sense they're not receiving updates posted from there.