I would not hesitate to use flannel for a quilt. I have used it for backing with no issues. I would certainly pre-wash in the hottest water you have and dry it to death in the dryer. Particularly if it's not a high-quality or thick flannel. And I agree with starching it to heavily if you're going to be cutting smaller pieces. As someone else said, it washes out after. It's only for stabilization. I would probably buy at least 1/2 to 1 yard more than required. I do this with just about any fabric anyhow. Gives me room for shrinkage; booboos and stash!