Wondering if I could get a hand.
I've played an MP game with a mate with me hosting and had a great time teaching him.
Saved and logged off.
Two days later went to play again, via MP with me hosting the Saved Game and now he can't see his correct CIV!
I've found the same issue on forums back in 2016/2017.
I have Utopia, Apocalypse, Plantoids, Leviathans, Synthetic Dawn, Humanoids, Distant Stars.
He has none.
He can't see his Plant race CIV but I can. I assume it has something to do with the DLC's that he doesn't have.
Interesting thing is, if he loads in SP the game that he saved just before we quit the first session, he jumps in as the correct CIV.
In the MP Civ Select Screen, if he opens the CMD Console and hits "play 1" it tells him he is the correct empire but once selecting either OBSERVE or another empire, has no control over CIV 1, just the civ he selected.
dlcs wouldn't matter
stellaris is nice about that
whatever dlc the host has, anyone in the lobby has access to it as well (or at least they should)
if there was an update for the game between when you saved and when you tried picking it up again; you may want to scrap that save
alternatively; host a new multiplayer game and see if your friends still has his Plant empire and if it is still working (i.e. the update from 1.7 to 2.2.7 pretty much made all empires non-functional for some reason, so they need to be fixed)
beyond that; your best bet would be to hit the tech support part of the stellaris forums; as a dev/moderator would be able to assist you more