I would soak it in cold water and a mild soap (Synthrapol if you're not sure of colorfastness) in the washing machine. Just stop the machine before it gets to the agitate cycle. Push down by hand once in awhile to work the soapy water through the quilt. Drain and add new cold water and soap daily. Drain, add cold water, hand agitate, drain, add cold water, hand agitate to rinse. After the final rinse, I would "block" the entire quilt.
If weather permits, you can block outside. Lay a large sheet on grass, lay the quilt on top of the sheet, and have a couple of people pull opposite corners to get the quilt straight in all directions. Lay another clean sheet on top and anchor the edges with stones. Allow to dry outside.
If quilt still isn't quite squared after it's dry, you can bring it inside to a carpeted area, lay on top of a sheet, mist with water, straighten and pin it to the carpet to dry again.
That's what I'd do because I think this is the safest way to clean the quilt. There probably won't be much shrinkage if you use cold water, and blocking while the quilt is still wet will also help. Even more than hot water, the heat of a dryer will shrink flannel quickly.
Even with unshrunk flannel, a quilt will not shrink if it is closely machine quilted. That is another option if you could stand to machine quilt it while the odor is in the quilt. You could even use a machine basting stitch if you didn't want the machine quilting to be permanent. For machine basting, I would use a crosshatch pattern with lines every 2 inches in both directions.