I know just how you feel. One of our new additions to the family decided to urinate in two of our vents while we were on vacation. I thought we were doomed. However, persistence appears to have paid off.
I use a combination of two different products when cleaning cat urine. Natures Miracle and OUT. I picked up Natures Miracle at my local pet store but I’ve also seen it offered in catalogs. The OUT I get at Wal-Mart in the pet products aisle.
Basically all I did was to take off the vent cover and using several damp paper towels (with water) and scrubbed down the surface of the duct work. I went as far as my arm could possible reach. Then I took a few dry towels and tried to mop up any liquid that settled into the nooks and crannies.
I then took a few paper towels saturated in Natures Miracle and scrubbed down the surfaces of the duct work. I let that dry (about 5-10 minutes) and then repeated the process. Once the duct work dried overnight I came back the next day to see if I could detect any urine smell. If I did I repeated the process the next evening.
Finally, after the surfaces had dried I used OUT for a final cleaning.
I tried reusing the vent cover but it didn’t clean well. So I purchased a replacement at a local hardware store and installed it.
No more scent and the cat has not returned to the vents again. Good Luck!
Sincerely,
Cris