Logs checked and real time monitoring had been performed, we found server to be unstable at higher populations of 60 players, the server would drop from 1500 frames to below 10 for over 5 seconds which causes desync.

Made a dev server and removed all mods and readded them one by one to try reproduce issue without changing any live instances of the game and to keep uptime for players.

Monitoring indicates that when players first load into the game the server frames drop.

When players join the server the NetworkManager (BI Sudios engine) cleans up by deleting files which causes a large load on CPS in turn causing FPS to drop due to trying to maintain 60 FPS for 45+ players.

This has also been reported by other community servers and confirm on vanilla servers.