i don't see why you wouldn't think it would work- I mix regular cottons & flannels all the time- tops, backs, mixed blocks, mixed cotton blocks with flannel borders, flannel blocks with cotton borders---flannel is cotton too- just softer. I do pre-wash my flannels when I am going to mix fabrics- but beyond that I don't worry about it. I even mix the 2 in raggy quilts - some blocks flannel, some regular cotton...no problem