I used donated flannel from JoAnns and I prewashed the yardage and it did shrink. I cut a length that was 6" longer than required to see how much it shrank. Then I made flannel crib sheets for a charity and had to make sure the finished sheets were the right size.
So I would say wash the size needed for your quilt plus extra, so you can make sure it will work well when your quilts are quilted.