I've run into numerous synch errors like the one you mention when playing on a lan, I don't know what the problem or the cause is but we never had this issue before the entrenchment beta, we've tried some crazy mods too.

We had differences as drastic as two of my planets being lost on my partners view and on mine they're fine.

Other more simple things such as his fleet crossing through the pirate world and being destroyed on my view but on his they go around.

This issue has put our play on hold sadly since it seems to happen every single game for us, it's just not worth playing a co'op game when you can't even help your partner because the enemy isn't there on your screen.... or even worse when you've destroyed them but they're not gone yet for your partner.