Hey,
A friend and I have been playing AI War for more than a year now and have been playing a bit more often lately, and we saw that dreaded DESYNC error twice already.
The first time it happened when we updated frequently just before the official release of Ancient Shadows, and yesterday it happened in a different game (we had to stop playing the other one) after we updated the game to 6.007-8. In both games, however, there is a massive amount of ships (in the Galaxy Stats panel, it indicates 31 000 enemy ships, but we know that in a planet there's a bunch of carriers with 53 000 ships inside them... we play 9/9 with an AI Progress of 500, going for the Fallen Spire alternate victory). There's no lag in the game, though, apart from when a few thousand ships attack a planet, but even then it's fairly smooth.
So we're wondering if updating when there's a LOT of ships is bad? Because we also just finished a game where the AI Progress was kept at 60 and we never had a problem with all the updates.
Yesterday, we just had to load a previous save file so it was fine, but once we were both in the game, the message "Waiting for players" was there for a long time for both of us.
The save file that with the desync is attached, but I guess I'll wait to see if our most recent save file also produces a desync before opening a mantis ticket (and my friend isn't online now so I would have to wait for his save file anyway, as per the instructions for desync errors).