There are other issues related to the saving mechanisms of the game but we are not sure what is going on with those yet. One tip that I have to avoid desyncs is to be sure that always when you are loading an existing game, it has the AI replaying their last turn before the players. This is the same as loading an autosave. The default save of multiplayer is simply copying/renaming the last autosave and this is the safest option. If when loading a MP game you notice that the AI does not replay their turn before yours, issues will probably arise as this was a "dirty" forced save which can be caused by saving twice and overwriting the same save. I am not sure why saving twice by default causes these forced saves, nor the reason why forced saves cause desyncs, but it is what I have observed.
Thanks for the explanation! What you're saying about the saving mechanism is quite interesting. Especially in that it conflicts with another issue I sometimes happen to experience. You're probably aware that sometimes when loading an autosave, the AI will not only repeat their last turn, but do two turns after another, skipping the human players. This is usually not such a big issue unless you're at war and get battered. The only way to prevent this double AI turn is by saving twice, essentially creating what you're calling a dirty save.