[Scorpius]

If you use jonesoft generic mod enabler you can disable and enable quick and painlessly. But if you dont then yes you will have to either scrap the mid patrol save and start the same patrol afresh or if you desperately want to use the mid patrol save, you will have to reinstall the game. Then load the save, finish it, and then whilst you are docked, install the mod and then start a new patrol.