Don't forget, your batting will shrink some too when the quilt is washed, perhaps enough to balance out any additional shrinkage from the flannel? Even though it will shrink a little more, the majority of the shrinkage should already be done with the first wash and dry. As long as the flannel piece is as big as your quilt top, I wouldn't worry too much about it. I personally love the nice dimpled old fashioned look when everything draws up a bit in the dryer.