Cut them apart, remove as much dead root matter as possible(all of it, if you can). Try to leave as much of the female(s) root system intact as possible, and be gentle.
Easy to say when it's not your grow.
TeaTreeOil answer is the best thing that you can do IMO.
Good Luck and let us know how it works out, I'm about to start my first aero set up like yours and have considered this scenario.
My 2 girls were in shock for 2 days... The leaves were hegging down and I was sure they were going to died..
But the 3rd day, just started to look better...
Here are some Pics of my girls now... they are doing great and smell yumm...
Cant wait to smoke them LOL...