The only sealer that I've seen used on flagstone was polyeurothane (sp?). It was very shiny, meaning very slick when it was wet; not good for a pool deck. My personal experience was stripping the old 'scarred' finish, applying the new finish, then slipping on it after a rain !
Is the material actual particles of the flagstone that have been broken due to water and possible freezing or is it the motar from the joints?
I would think that any sealer would have to be pretty thick to stop 'sand' from coming off of it, but...
Do you have a salt water chlorine generation system by chance? I've heard of problems in this area with the salt water dissolving limestone rocks. But I don't know of a good way to seal the surface without creating the slippery surface mentioned above.
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