I got it worked out. With help from the discord, I deleted the offending formation from the DB and it all works fine now. I now have ~1 million new slaves citizens.
If anyone's interested, it was a single xenoarchaeology vehicle that was somehow impossible to kill.
How does DB editing work? Are there any resources available for that sort of thing?
DB editing is strongly discouraged, don't report bugs if you mess with the DB.
There is no such thing as strong discouragement from editing the database... as long as you know what you are doing that is just fine.
Sure... don't report bugs on an edited database... make sure to replicate any issues in a standard DB before doing so.
If Steve had wanted the database to be not messed with he would have put a password on it. He used to have that but usually gave the password to anyone who wanted to have it that asked for it... as long as you understand that you can potentially corrupt a game by messing with the database then go right ahead and do so.
You can just search Google for any free database editor that is out there to do it, should not be hard to find.