If you do, I would make sure that you pre-wash in HOT water and dry both of them. I usually pre-wash/dry flannel twice. Flannel is notorious for shrinking a lot and if you don't pre-wash it will shrink more than the cotton and you won't like the end results.
I think it might be neat to see the different thicknesses in some blocks ... like a pinwheel or an Ohio star with the stars in flannel and the base in cotton.
Also suggest reducing your stitch length (more stitches per inch) and using lots of starch (easier to iron the flannel from the back and don't forget to let the starch "set in" before you press it).