Hi Stacey, I can relate to your problem. I have a male and female both 3 yrs old who were best buds. One day the male got territorial with the female, started attacking her and chasing her. Then to add to the problem, I adopted a stray older male (vet thinks he's about 12 yrs old) who is aggressive to the other two cats. I've used Feliway and some Bach Flower remedies, which have helped. But the behavior still flares up. The vet said it can take up to 6 months for the cats to work out their social interactions, and it's been 6 months.
Is there anything besides separating the kitties that you can do to calm the aggresseive behavior?