Just for clarification, are the trays open top, high sided, enclosed, or a mixture? It may help others give more appropriate suggestions.

Could it be possible that he was ambushed in the tray once by your other cat and now only can go when he knows the other cat is excluded and you are protecting him?

Obviously, there has been a traumatic experience in his life. Whether it happened at the litter box, who knows. You have another cat who may have been a culprit! Because this has been going on so long and medical problems have been ruled out, you are going to have to retrain your kitty and help him feel more secure in your home. Stress plays a huge part in a cat going outside the litter box. Cats are perceptive and smart. There is something going on there. Maybe a cat behaviorist could be of some help. You have plenty of trays and he goes when you accompany him. He sees you as his safety net. I'm really guessing something happened between him and your other kitty.

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The little monsters 3

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The little monsters 3

If the blood continues, it's back to the vet again. There needs to be a thorough examination of that part of your kitty! I think you hit the nail on the head with your other kitty! There is something going on there and their relationship has changed. Refusing to use a litter box the other cat has used -- cats have 14 times the smelling power we do, so he's not liking something there. It can seem perfectly clean to you, but it's not to him. It's obvious you have to keep them separate as far as using the litter box. However, it's wrong to keep one cat locked up in a safe room and the other cat has the run of the house. These two are going to have to get along together. Sounds like you need Jackson Galaxy and appear on an episode of My Cat From Hell. There is always a solution to your situation. Many people do not want to spend the time required to figure this out. If you're willing to spend the time .... it will get better. You can search for cat behaviorists online and see what you come up with. It would be great to have someone in person who can actually get acquainted with your kitties.