I take it both your cats are spayed? Her cystitis may also be ideopathic and stress related - especially if the male is giving her a hard time. It may be an idea to invest in a couple of plug in Feliway diffusers to help her feel a little calmer and may be put some Bachs Rescue Remedy in their water. Clean any areas where she has peed with biological detergent and try using some of this spray
Urine-Hater. Eliminates Urine & Pet Odours - £9.99 : Pinky Pawz - Simply ... the cats whiskers!, Pinky Pawz - Simply ... the cats whiskers!
This really helps eliminate any odours and hopefully stop her going back to the same place.
Good luck - let us know how she gets on.