I wouldn't take anything apart. I would hand applique new points over the frayed ones. Flannel is not that hard to work with, but I would wash and dry any new flannel several times to make sure it is through shrinking before cutting out and appliqueing the points. If you can't find flannel fabrics that match the points, perhaps look for good contrasting flannel and simply applique over all the points of the star to make them symmetrical. If you are covering up any hand quilting, I would do a little hand stitching over the quilting (perhaps working from the back).
If you are ambitious, you could make him a new flannel quilt too so that next year he can leave this one displayed over the back of a couch to preserve it a little longer.