I have mh suspicions that this is some kind of deadlock issue. After fucking up my config during am upgrade (too many database connections, too many workers) the new multithreaded federation thingy seemed to become quite unstable. From what I could tell, the threads that are supposed to deal with federation all broke/shut down, but didn’t get automatically restarted again, leaving some messages and instances in limbo until the entire server got restarted.
After fixing my database connection issue and reducing the amount of workers, I don’t think I’ve encountered many issues since. I occasionally click the little icon above a post to check if my response had reached the community server, and usually it does, pretty quickly.
This issue sounds awful to have to debug, best of luck to the Lemmy devs in finding a fix!