It is my understanding that in making pieced quilts, cutting on the straight grain of the fabric is not as important as if you were making a garment. Since you cut the fabric up in little pieces anyway, the grain of a particular piece may be pointing in any direction. Years ago I was taught to find the straight grain of the piece, trim the fabric on the grain and then try to even up the selvages from there. Sometimes impossible.
I just opened a jelly roll that doesn't have pinked edges, so it is clear whether it is cut with the grain or not. It not only isn't with the grain, it seems to be about 20 degrees off. Sheesh! All those little raw edges are waving like fringe. I don't think it will make a difference in the quilt, using them as they are. If I tried to cut them with the grain now, I would end up with about 1/2" strips rather than 2 1/2" strips.
So, just do the best you can. The flannel should probably be washed before cutting anyway. It might even up a bit after laundering, and show it's true self.