Federation Bugs are still around, and this is no exception.
Try going to the "search" button, and copy/paste the comment's URL into the search bar. This will force the lemm.ee server (literally the software) to try to fetch that comment specifically. From then on, the comment should be "known" by the system and stay up-to-date from there on.
Then again, it shouldn't have desync'd in the first place. So there's clearly some kind of obscure desync/federation bug happening.