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I can only think of one solution: seperation. I don't think this is something that's going to change if both are in the house for so long. Maybe they're just very unhappy and can't tolerate the situation. Is rehoming of one of them an option? It sounds like a very big problem.

I once had to rehome a male cat who couldn't tolerate another my other 2 cats. It broke my heart, but it was the best I could do for him. He lived a very happy long life as a single cat.