Hello, my name is***** and I have over 20 years of experience as a veterinarian. I'm sorry to hear that your cats Bundy (big guy) and little girl are suddenly not getting along after a stressful event and I'd like to help.
Cats in the wild don't normally live together. They compete for food, reproduction, and sleeping areas and often fight. In homes where the resources are endless they may learn to live in peace and sometimes actually enjoy company, especially with a dominant kitty that doesn't allow discord. When animals suddenly change their attitudes toward one another it means that something has changed. Either there is some sort of stress in their lives, resources are less or someone isn't feeling well.
I know that this started with some sort of stressful event one night but because it hasn't resolved and one cat ended up so afraid that he/she urinated there may also be an underlying health issue. Ideally both should have a thorough physical examination, urinalysis and bloodwork to make sure all is OK. Cats are very good at picking on the one who is weak in the group. It's also possible that one has an undiagnosed health problem which is making Cal the target of his housemate's attacks or Ali more grouchy. Cats are very keen at picking up a change in body odor which can signify sickness. Make sure their urine is checked for any signs of crystals or infection and cultured to make sure a subclinical low grade infection isn't part of the problem. Bloodwork to look for internal organ disease and hyperthyroidism is advisable too. It sounds like this has been done.
If all is OK physically and they are still fighting then this may be purely emotional or environmental stress related.
It may be a change in the home environment, or even outside animals or pets in the homes around you that led to the event. If one or both are stressed by a stray animal or wildlife outdoors they can take it out on each other. This is called displaced or redirected aggression.
If you think it is related to something you can change do so, block doors and window access and play soft music or the TV when you aren't home or at night to block outside noise. You can also use a product called Feliway which is a synthetic version of a feline pheromone used to mark things as "home" or safe. This can be purchased at large pets stores or on line. It comes in diffusors, sprays or a collar form that has impregnated pheromones that they can have with them at all times.
You might also try using a product called Bach's Rescue Remedy. This is a homeopathic remedy that can calm them down enough to learn to live peacefully again. It is a liquid that is added to the food and/or water.
If those things aren't working for now I would keep your two separated, especially when you aren't home, just in case. We need to give them both some peace while we get this sorted out. I would use the same brush on both so that their smells are familiar to one another. Rotate beds and toys between the two areas so that nothing becomes one kitty's only.
Make sure to have plenty of cat perches or condos and toys so each can have their own place to rest and things to play with when you do bring them together so there isn't competition for resources. I am glad to hear that each has their own litter box but there should be one more box than the number of cats. That gives them a choice, allows either kitty to urinate in one box and pass stools in the other, which some cats prefer.
If either cat starts to stalk or attack use an airhorn to startle him. An immediate negative consequence that is always present and not physical may be enough to help change behavior.
If these measures aren't enough you can discuss oral medications with your veterinarian as well such as fluoxetine or amitriptyline as calming agents to decrease the stress and aggression. These don't need to be forever, just until we can settle them down and they learn to live in peace again. They can be formulated into flavored liquids or a paste that can be applied to their ear skin and absorbed transdermally. Although the transdermal absorption route isn't perfect, as it is less consistent and reliable, it can be a viable option when owners cannot medicate their kitties orally.
I do find that when cats that previously got along fine, and now things have changed, that either medically or socially there's been a shift. It can be difficult to figure out and fix but that's usually the only way to restore peace. Best of luck with your kitties.
Let me know if you have any further questions.