Now, when I tried to load it up, I have two instances in the list of my region4 fortress - one is the copy as it was when I saved at work, one is as it was after the several hours of play at home. Looking in the files, it looks like it saved the later .SAV overtop of region5 - so now I have a region5.sav that goes with the files in the region4 folder, and the files in the region5 folder are for a .SAV file that doesn't exist anymore, and the region4.sav is not the most recent save.
I have not tried renaming folders and files again to try to get things to match up properly again. Should I? I was thinking I could try copying my more recent save to a new region6, and restoring the original region5, and see if that works. Not sure I want to mess with it until I know it should be working.
I would have expected what I did originally to work - I didn't see anything that looked like a master index of saved games. I have backed up that save folder, will probably just nuke the folder itself and start from scratch for now.
As far as what it should actually be trying to do, I suppose it should try to use the filename it had when you loaded it to search for its appropriate folder.