i mix flat cottons and flannels all the time- been doing it for years- flannel gives wonderful texture to a quilt- whether it be used as appliques, sashings, borders, blocks---it is soft, fluffy and great to use-
sometimes if your cottons are thin you might want to add a layer of muslin to them to make them as heavy as your flannel- but it is not always needed- and sometimes it is the flannel that is thin and needs a bit of foundation- but they work very well together