Note that the Dominions 3 map editor will delete all special commands from the map, so don't use it to modify any map with scripted stuff or you'll lose that.
Easiest to do is make a copy of the map file, edit the copy, save it and then copy-paste the neighbors stuff into the actual map file.
Edi- not exactly sure how to copy-paste the connections. And I'm at least somewhat certain that the map in question didn't have any scripted stuff (though how would I make certain?), so I just removed the offending connection from the map itself.