One of my kitties once peed on a quilt I was halfway thru hand quilting. Besides the "ick" factor, the smell was so bad I seriously considered throwing the whole thing in the trash. But thought I'd give washing it try.
What I did was put it in a pillowcase, and wash it in a front loader down at the laundromat. I didn't have a front loader at the time, and thought it would be less turbulent than the agitation on a top loader.
Even though i had to wash it several times with a variety of different products to get the smell out, It worked fantastically. My basted layers stayed perfectly put, and I was able to continue working on it.