Braid,

There are several thing I would do to this floor :

1 . first strip the floor to remove any finishes that have been applied ( if there is an acrylic on it it will strip fairly easy , if it’s an epoxy or urethane it will be much harder and will require aggressive stripper)

      When a floor has a coating on it I recommend a single edge razor blade to check the finish, if when scraping the floor the finish kinda of rolls off the surface it usually an acrylic finish, if it fake off it will fall into the epoxy or  

       urethane  finishes and will be much harder to remove.

The single edge razor is your best friend when checking topical coatings.

2. once the floor  is stripped and cleaned I would then go over the floor with a honing powder, depending upon the finish your customer is looking for  I would use either a 250 grit or 400 grit powder, this will expose new stone and should eliminate the white water damage you are now seeing.

If the moisture problem is not corrected it will occur again, if a topical sealer is used you could compound the problem down the road.

I recently used the Stone Care Central Color Enhancer and was please with the result.

The product I prefer overall is the Stone Loc from Richard James chemical . this will do everything you are looking for once the floor is properly cleaned and prepared. This seal will stop the shedding, it will enhance the  color and will allow the stone to breath, this is one of the only coating that I know will allow the stone to breath.

When applying this you must follow the manufactures  instructions to the letter. I have used a product like this made by the same inventor on over 50,000 = sq ft in my past , and only had 1 small failure , not do to the product it was due to the technician not following the instructions.