I'm sorry that your question wasn't answered in a timely manner. I'm sorry to hear of this with your cats. Aggression may occur between two or more cats already present in the household where there had been little or no previous history of aggression. Relationships may change as cats mature and age. In addition, increased conflicts may arise when there has been a change in the social group (people or animals becoming a part of the household or leaving the household), or when there have been major changes to the environment like moving house, allowing them outside in this case, or more subtle changes such as where the cats sleep, eat, perch, or eliminate. Medical problems could lead to pain or irritable-induced aggression, or may alter the way the cat interacts with other cats in the household. Any event leading to redirected aggression* could also lead to a change in the way that cats interact with other cats in the home. It's also not unusual for aggression to arise when a cat has been out of the home and then returns (e.g., from a groomer or veterinary hospital stay). This may be due to pheromonal alterations (pheromones are chemicals that cats secrete in order to communicate with other cats), anxiety or discomfort of the returning cat, or the response of one or more cats that remained in the home to some alteration in the way the cat looks, acts, or smells upon its return. There may also be territorial and status issues that need to be re-established, even if the departure has been relatively short. Many of these problems are mild and will resolve themselves over time, particularly if there is enough space, perches, and hiding places for the cat to avoid interactions while they again "recognize" each other and re-establish a compatible relationship. This may take anywhere from a few hours to several weeks for some cats, while on rare occasions the problem may be sufficiently intense to require a formal reintroduction program of desensitization and counterconditioning in much the same way as a new cat is introduced into the household. It may be prudent to continue sequestering one or both of your cats in a dim and quiet area until their level of arousal abates. Many owners will then “test" their cat(s) every day or so and continue sequestering them if necessary.
*Redirected aggression is diagnosed when the target of their aggression (each other) is not the stimulus that triggered the state of aggressive arousal. Territorial, fear-induced and defensive aggression are the types of behaviors that are likely to be redirected by them. Stimuli that can cause an aggressive state of arousal include the sight or sound of another cat (at times quite far away from the home), unusual noises, odors of other animals, unfamiliar people, and unfamiliar environments..all of which might be directly related to their having been allowed outside. A common situation is one in which the pet becomes aroused upon seeing or hearing another cat while sitting in a window. When the owner attempts to pet it, pick it up, or nudge it away from the window, it attacks. It may show aggression toward another pet when approached in similar situations. Redirected aggression is a common cause of the sudden appearance of aggression between cats in the same household that have been living together amicably for quite some time. This type of aggression is probably the most dangerous type of aggression cats exhibit due to the uninhibited nature of the bites. Treatment involves identifying triggers for arousal and then removing the pet's access to the stimuli. You may have to be quite the detective as stimuli can be imperceptible to owners. Medication can be beneficial for reducing their response to environmental stimuli - psychoactive drugs such as Prozac have been used. The most important thing that I can impart to you is to be careful around them when they are aroused. Too many of my owners have ended up in the hospital due to infected bite wounds. One encouraging fact is that many of our cats will habituate to the arousing stimuli and "self-cure" within weeks to months.
You can't force the issue. You can't make a cat like another cat. Formal reconditioning involves playing with, feeding, and rewarding them with treats when they're both present. This is best done while he's leashed for their protection and it involves more than person. It's time consuming, can take weeks and months, and isn't always effective. The most expedient manner in which to address such aggression within a household is often by restricting cats to certain sections of your home as you're doing. Please respond with further questions or concerns if you wish.