It's likely the roots are too intertlaced to seperate without severe stress. I would sex them (cut the lights back to 12/12 for a few days) and see if either is a female. If so, keep her. (cut the other one at it's base) If both are female, save the one that fits the strain profile the best, or the healthiest one.
If both are male...you can either keep one going till you harvest some pollen for making seeds sometime down the line, or kill 'em both and plant some new seeds. (one per pot)