I work for Fiber-Seal here in the metroplex, and my professional advice is to replace the cushion with a brand-new one. Contact the manufacturer with the model number/type of sofa, and they should be able to mail you a new one for a nominal fee. The leather, if pigmented, should be fine with a good pet odor deodorizer from a pet store.
More than likely, the smell has embedded itself in the cushions, and those foam pockets are just too many and too tiny to allow all of the urine crystals to go away.
If you would like me to take a look at it to see if there would be anything else that our company could do, please give me a call at ###-###-####. Good luck!
B. Biehl
www.FiberSeal.com