in the 100+ quilts i've made over the years i would venture to guess 3/4 of them have had flannel backs-i love working with flannel- and everyone around here loves the soft-warmth
it is certainly nothing to be afraid of- it's just another cotton fabric=
it does have a looser weave- so pre-wash it-
when i buy my flannels i bring them home - toss them into the washer- with a small amount of detergent to remove any sizing/chemicals in the fabric- warm water- then i toss them into the dryer-
when they come out they are (tightened up) soft and wonderful-
it is a good idea (especially if the flannel is single sided-or thin) to starch your flannels before cutting-this just makes it easier to get accurate cuts.
some people wash their flannels 3 or more times---i never have- i wash & dry them once and use them- if i'm using them for a raggy quilt i don't bother pre-washing
i've never had a flannel backed quilt come out with any type of problem---from shrinkage-or anything else- they are beautiful, soft and cozy warm.
i use flannels for appliques- with no adverse effects either-
and it quilts beautifully too- i've just never had any problems with flannels- it is one of my favorite quilting mediums-almost all of my quilts contain some flannel- on the front, for backing- even as batting