For VotM what you can do is copy the RuntimeData/Expansions/5/ folder from your steam AIW install, to a thumbdrive or something, then copy it from your thumbdrive to your AIW install after the wipe.
Or, to cut to the chase, you could just copy the entire "AI War Fleet Command" folder from steam to the thumbdrive. If you want to remove its steam capabilities just delete the steam_api.dll (or whatever it is) from that folder.
It will even run from the thumbdrive, on windows or mac, and as usual it stores its save files inside that folder. Though naturally you'll get better performance running it off a normal drive.
Let me know if that doesn't address your use case