I have had to undo Elmer's glue on backing/batting, I just use my spray bottle of water, get it good and damp (not soaking), let it sit for a little while for the glue to get soft and then gently peel the layers apart.
For me I would have to re-do it too. Just a good soaking, then wash and iron the backing fabric and all will be fine. Appliqué won't change the texture of the wrong side of flannel.
