Denim wears forever; consider how long blue jeans last! Blue jeans out of flannel would wear much faster (especially in the seat and along stress seams).
I would be tempted to simply add another flannel backing to the existing backing. It would be easier than picking the quilt apart, and what is left of the current flannel would provide a buffer between the denim and the new flannel. I would definitely pre-shrink the new flannel several times to get the weave as tight as it can go.
I would check with the owner before substituting quilting cotton for the flannel backing as they may have a strong preference for the flannel.