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I've noticed something similar on my instance in some cases as well. Nothing obvious logged as errors either. It just seems like the comment was never sent. In my case cpu is minimal so it doesn't seem like a resource issue on the receiving side.
I suspect it may be a resource issue on the sending side. Potentially, not able to keep up with the number of subscribers. I know there was some discussion from the devs around the number of federation workers needing to be increased to keep up, so another possibility there.
It's definitely problematic though. I was contemplating implementing some kind of resync this entire post and all comments via the Lemmy API to get things back in sync. But, if it is a sending server resource issue, I'm also hesitant to add a bunch more API calls to the mix. I think some kind of resync functionality will be necessary in the end.