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I mentioned the other day that requests to walledgarden error (curl says 'transferred a partial file'). If another instance doesn't get a good response for these requests, then after 3 days, it'll mark the other instance as dead, and not federate out to it. Once this happens, it's a pain, because traffic from walledgarden doesn't make them realise that it's actually alive, you have to wait until it tries again and gets a successful response.
If you haven't done so already, it might be an idea to use curl to query your site, and see what the response in nginx says.
Update to this-
After talking with my host some adjustments were made that should correct the curl error. I still don't believe this has anything to do with the lost sync but it's one less thing to worry about. Thanks for the information and help!
I saw your comment but I was mainly concerned with getting the instance to show up on lemmyverse at the time, which I suspected was the connection being blocked by our host (it was). Coincidentally since getting listed lemmyverse has been having its own problems so I put it on the back burner.
I'll do some deeper digging into this and see what I can figure out. I don't think it has anything to do with the communities falling out of sync since it's never mattered before now and WG isn't the sole instance being impacted, but it should work correctly either way.