i mix textiles all the time in quilts- flannels and flat cottons work great together-
the only things to keep in mind is- flannels tend to fray more (they are a looser weave)- starching makes cutting easier and more precise-if you are using clothing- all the pre-shinking has been done- so i wouldn't worry about that-
if the flannels are thin you can use a stablizer
cottons- and flannels get softer, cozier with time/use/and washing/drying...make FABULOUS quilts