Oh my... I would try acetone and a scrub brush. Make sure you reseal after using acetone.

I have Belgian Blue Limestone countertops in my master.... I use ONLY a French Soap on it. It's a liquid form of soap. It's worth a try and there was a lot of info I researched before I started using it. Let me look for the name.

http://www.lesavonniermarseillais.com/home-care/savon-noir-100-natural-all-purpose-olive-oil-soap-33-81-fl-oz-1-liter-fragrance-free.html

Not sure if it will do the trick, but it works very well on mine and seals it nicely after buffing. I know this the the outdoors, but just thought I'd toss it out as an option.

http://www.burgundylimestone.com/maintenance.asp