SS+*, II*, BRDY, Common Radar, the Libs. Freshly downloaded Console Commands and Save Transfer. Asterisked mods needed updating, so used Save Transfer. Started with an all-BRDY fleet, ended with everything proper except three copies of the same Cetonia (freighter), possibly around 200 extra elite crew (I had some in Blackrock's storage, I don't think that many, but entirely possible I'm wrong), and all weapons are missing; the terraforming station is empty.
I have backup copies of the pre-update mod folders, save, and Save Transfer output if you want me to debug or send you something.
EDIT: Went back in time to check. 109 elite crew in cargo, 81 in Blackrock storage became 352 (109+81*3). 954 food in Blackrock storage was also deleted. The triplicated ship was in Blackrock storage as well; this leads me to think that and the crew inflation is caused by Blackrock (planet), Lodestone (moon) and Port Augustmoon (station orbiting Lodestone) all being one "entity," i.e. they share a market no matter which is docked at like the Imperium capital. Can't explain the complete wipe of weapons and food stockpile.