Turned out that my machine had memory issues.

Thanks go to @boskid for helping with debugging issue.

I took spidertron packed with rockets and went north to biters' villages. Rockets started, I put lot of artillery points and then game desynced again.

https://marcin.juszkiewicz.com.pl/test/ ... -35-55.zip

Feel free to connect and try to reproduce.

Some minutes later another desync and game crashed quietly after reconnect button press.

Restarted, tried to connect and got "user with your name is already in the game" message. After retry it connected.

I have Factorio running on my own Linux server (Debian 'buster') where I have one simple game without any mods. Joined game in the morning, expanded base a bit and had to leave home. Left game running and when I was back I saw desync information. Reconnected and left game. Server output: 2020-09-17 ...