Use Radmin VPN or ZeroTier instead of the Uplay/Steam relay. This fixes 90% of desync issues regardless of mods.
The Gilded Current: On the Art of Remaking Perfection Anno 1404 Venice Mods
Throw away the old method of replacing data/config/game files. The modern way is created by community legend Flack . This tool allows you to toggle mods on/off without reinstalling the game. Use Radmin VPN or ZeroTier instead of the Uplay/Steam relay