I'm trying to figure out where the Moonbase Commander saves are located. It doesn't look like the saves are in the game's own directory.

https://steamcommunity.com/app/254880/discussions/0/558747287450310275/

I'm a little confused, since when I play the Challenge mode it's clearly doing some kind of "auto save" after each mission is completed. It shows a medal and then the next level is unlocked. This information isn't available in a separate file?

It saves your rankings in the Challenge mode, so yes, it's probably in a separate file, but I don't know which one.
Or maybe it is in game settings.

I checked the "user" folder in the game's directory, but that only had replay info and from what I can tell no actual save data. I also checked pcgamingwiki.com but there was no save file data listed there.