Received. From the save file, it looks like the save/load system was, as usual, the problem.
To resolve the previous problem, each location stored a list of all locations it was connected to as just integer indices into a big list of all locations. It then deleted its links, and when the game was loaded it restored them based on this list. I forgot to clear the list each time, however, so it was storing duplicate links.
In the short term, this had no impact. Location A was connected to location B, it just happened to be connected twice. No real change in behaviour, units could just choose which connection to use. With sufficient links, however, it must have slowed the pathfinding down to a crawl.
Bug fixed, along with the infiltration one (thanks to my co-author for that bugfix), and a third I spotted in the voting UI (go-to-self button calling wrong function).
New version should be uploaded now.