Wipe the flagstone with a damp cloth to remove all dirt and debris. Allow the area to dry.
Cover areas adjacent to the flagstone with tarps to protect them.
Apply a sealer stripper intended for the type of flagstone surface you have. Apply it with a paintbrush, and ensure that there is an even coating over the entire surface.
Wait for the sealer stripper to work. The specific amount of time to wait depends on the brand of product you selected; follow the manufacturer's directions.
Scrub the surface with a stiff-bristled brush to lift up the sealer, unless the manufacturer directs otherwise.
Mop up the sealer stripper. Dip a clean mop in a bucket of water and rinse the floor well.