I would wash the flannel first.

And don't forget that flannel often distorts with washing and drying. I have never had a piece come out square after washing---I have always had to square it up again.

Thank you all for taking time to answer my questions! You've given me the guidance I was looking for.

I would always pre-wash a flannel back unless the front is also unwashed flannel. The few times I did not, I was tying a quilt using top of the line printed flannel. I've had uneven shrinkage and dye leakage on small projects using woven flannels (plaids) and lesser quality flannels when quilted.

It is best to pre wash a larger piece of backing fabric this will make for a better fitted back.I would not wash front cotton and not back as when the back shrinks in tbe first wash it will cause the top to not lay flat very well. So many variables..