It's fine to not pre-wash flannel ***IF*** you do a lot of quilting. Quilting means that the quilt will shrink only as much as the batting allows. If the quilting lines are far apart, the fabric in-between quilting lines can shrink at a different rate than the batting.
I would go ahead and use all of the flannel unwashed and just plan on doing a medium stipple or similar-weight quilting design. My batting choice for this would be Hobbs 80/20, which has about a 3% shrinkage rate; however, other battings could work well too.
The reason I know this will work is because I attended a class with Harriet Hargrave, queen of eliminating pre-washing. So many quilters wouldn't believe that pre-washing was unnecessary, she made a flannel quilt to prove it. She *did* do a reasonable amount of quilting on it. Anyway, she measured it before and after washing and got something like 1/2" of shrinkage. She also had the quilt with her, so class members like me could closely examine the quilt. It looked fine.
The thing is, fabric shrinks differently when washed all by itself compared to when it is quilted to a batting. When closely quilted, fabric cannot shrink more than the batting; the batting controls how much the fabric can shrink.
One thing I would do with flannel, though, is spray starch all those pieces. Starching makes flannel a lot easier to sew without distortion.
Also, you still may want to test the fabrics for colorfastness. HH does this by placing a small piece in a glass of water for a few hours to see if any dye bleeds into the water. After that, she rubs the damp fabric against a piece of white to see if any dye "crocks". I would probably dampen a piece of white fabric and rub gently only on "suspicious" fabrics to see if there is some transfer of dye.
For the first washing, in order to guard against any bleeds, I would use either a home top-loader washing machine or a large laundromat front-loader with Synthrapol. You want lots of hot water and Synthrapol so any stray dye particles stay suspended in the water until rinsed away. Dry immediately, so one damp fabric does not lie next to another damp fabric for any length of time.