Have done that before quite often, because my friends and I tend to play VERY long PBEM games, which offers some opportunity to import new rules from time to time.
I'm using the Civ Multi Tool (Save Game Editor) for that. First, export the map and save it somewhere. When you open it in the editor, be sure to add another player in the Map options (Player Settings, Number of Players) or it will crash. So if you have 4 players in the save, raise the number to 5 in the editor before scrolling anywhere on the map. Import rules, do what you like to customize the map, and save the map in the Scenario folder. If you do it right, you'll be able to choose the map from the game menu ("Civ Content").