I didn't realize the save files are plaintext at first. I found the VESSEL section for the space station and deleted the parts that make up the ship that should have decoupled, then gave myself enough money to build another one of those ships so my problem is solved. I'm going to file a bug report, but if anyone is curious here is the screenshot and save files (it's the "Kerbin Space Station" that's orbiting Kerbin):
Screenshot
https://www.sendspace.com/file/izix0b