That's a very good question. It stands to reason that the flannel would wear more quickly, especially along the seams. Flannel is a much softer fabric. I wonder if you could put a layer of muslin between the top and new back and if it would make a difference. Was this quilt tied or quilted in some way as well or was it just birthed? If it was NOT, I would be tempted to at least tie it, to keep the the fabrics rubbing together, to a minimum.