Rotting Roots Please HELP!!!!!!!!

Have I messed up? I'm growing in three gallon pots. I've got two seedlings in each pot I figured this way if one was male I 'd be left with one female per pot and if both were female . Hey so what. Obviously I will have to chop the males down at soil level. Will there roots go rotten and cause problems. I did the same thing in a Hydroponic setup a few times and had no problem. Will soil be different. Please advice as I am concerned it is to late to replant as the roots will be intermingled. Plus with one pant per pot I'd be lucky to end up with two or three females.

 

Most root balls from cut down plants will do no harm to other roots especially ones from young plants,they simply die off and supply nutrients while decomposting in the soil as organic matter.Not really a good idea to place seedlings in such large containers or multiple plants in a container as hard to maintain correct moisture balance,as well as plants fighting each other for nutrient uptake,multiple transplanting is much better in the long run for the plants overall health.