Here is the save.
Okay, I have figured this one out. There were a couple of really longstanding bugs with how the game loaded a save that had objects heading for a transport in them (not in a transport, but scheduled to get in one). There was also a bug with loading some player stats in some circumstances, but I'm not sure why that was coming up here. Neither one of these particularly seem to be related to the recent prereleases, I'm pretty sure they were present in 1.201 or even further back, it may just be that no one has ever saved right at the time needed in order to cause this issue. Anyway, is fixed for N, and the Threat is down to around 1,100 when I load that. The high threat before was most likely due to it not loading other parts of this savegame correctly.