I generally clean flagstone with 1qt.of muratic acid to a 2gal.mop bucket full of water and scrub the grout lines and the stone with a stiff plastic bristle brush.Then rinse the stone. After that I use bleach and water and do the same process over again,Then wait till the area is dry. I would wait 24hrs and then apply the sealer.Hope I was of help to you . I know this will work . p.s.clean it about once every 3months with the bleach and water to maintain a beautiful appearance. steve.