You can copy/paste the folder somewhere else and run it from there, i have it set up like that. Mine's on the desktop
Be extra careful with the folders in Documents\My Games\ though, Freelancer and Discovery, i dont know if theres another way to keep them safe, but i copy them onto the desktop each time before i run the modded one, and paste them back into the My Games folder when i'm done - im also not sure if messing these files up still gets you banned, it used to be an issue in 4.86, but i'm not seeing it happen anymore, though i still wouldn't take any chances