Yes, desyncs have had quite an infamous history in Sins. The Dev Journal does the best at explaining it as well as the kind of thing that can cause it. While most of the big ones have been fixed, a couple of the desync prevention strategies developed before my still be relevant for this one.
1. Disable autosave: while if you get a crash this makes it more damaging, historically this could prevent some desync bugs.
2. Restart Sins after every game. Again this is probably fixed but for a time it was by far the best method to prevent desyncs.
Also are you using any mods? While its pretty rare for mods to change things enough to cause them, it is possible, and as most mod teams do not test their work online and certainly don't have the manpower to fix one if it comes up, it may not be known.
