I would knot the thread, use it in the seam allowance, and tunnel stitch it shut. For the tunnel stitch, slip the needle through the fold of one side and then catch the other side, then tunnel thru again. When close to the end, I would pull the thread and it will close. I would try to use a small knot then and pull it through as if you were hand quilting. I do this a lot and some people look at it and ask where I stitched. Try it!