My wife and I play on a server I set up, but about 66% of the time one or both of us becomes invisible, and no amount of rejoining, kicking, teleporting, rebooting, or anything else (including MRForceVisible) will make one or the other of us visible again. Kinda killing the gameplay completely. Basically unplayable. 
Java or unity version?
In the Java version, players become invisible if you didn't receive any new sync packets from them for a given amount of time (IIRC the threshold was 10 seconds). Player sync packets are sent via UDP, so if you don't receive any player sync (but if all other stuff like world generation etc works fine), this means there must be a network issue regarding UDP. It could be either a clientside issue (most likely caused by a firewall) or a serverside issue (in this case it's a bit more complicated and depends on whether or not this is a locally hosted server). If it affects both of you, it sounds like a server issue...
You could try to join a pulic multiplayer server and see if you experience the same issues there. If you still cannot see other players, it's very likely a clientside issue - in this case I'd recommend to have a look at the firewall or antivirus program (probably it interfers with the game). However, if you don't run into this issue on other multiplayer servers, it's probably caused by the server (if there is a firewall running on the server, this could also be the culprit).
This sounds like it will be "fun" to trace. I don't really have special AV/Firewalls on any of the machines beyond simple Windows Defender and Windows Firewall. Ports are opened appropriately. We can at times see each other, so I'm pretty certain that firewall is not the problem otherwise we'd never see each other. Since I have no special AV, and Windows Defender thinks the program is fine, I'm pretty certain it's not that either.
Just try what red suggested. Go to another server and see if it's the same there.
Eliminate the possibilities.
There’s a joke about UDP. It goes like... never mind, you probably wouldn’t get it.
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