This is what I do when I use flannel as a backing...it is warm, soft and cuddly.

Just did this recently for an oversize twin quilt and had no issues. I pre wash all my fabrics. Didn't have any more issues with threads/strings on the flannel than the regular cotton. I don't have a walking foot but had no issues when sewing the binding down to the entire quilt. I machine sew my binding to the front then hand sew to the back. I think the flannel was actually easier as a backing during the machine sewing phase since it slides easier than the regular cotton. The flannel I used was a nice heavy flannel by Moda. Would definitely recommend this fabric.

Thank you all so much for your encouragement. I hadn't read anywhere, where this was done so was wondering if it worked & OBVIOUSLY it does. I can now put flannel on the back of my quilt(s) & not worry that I have done something disasterous.
Jennie

I love flannel on the back, so warm and cozy!

I was in my LQS recently asking about this very thing. My question to the experts there (they really are experts in my opinion) was can I use both flannel and regular cotton (from old shirts) in the same rag quilt? They said yes IF I wash it thoroughly. They said to be certain, wash it 3-4 times and then dry...
Happy Quilting!!

i NEVER pre-wash my flannels more than once, i've used flannel in peiced tops and for backs on probably a hundred quilts...have NEVER had any problems with shrinkage after the quilt is made. the batting and the density of quilting also dictates how much a quilt will shrink...regardless of the fiber content of the top/back. i kind of feel like some people worry way too much about silly things.
that being said...if you purchase, single sided, thin flannel it may shrink more than a quality flannel