I have done a number of flannel quilts also. Biggest thing is to be sure your seam allowances are ample--Flannel tends to raffle more than plain cottons. Quilting flannel is generally heavier weight/tighter woven than shirt/pj flannel.
I do not prewash them, just let the family wash their own, which they do a lot of. One I have had to mend seams on, but I just did more machine quilting right over the seam area and it worked fine.