Hi, max m!
The first thing that I would do is to get a second opinion by someone to make sure of what kind of stone it is. There are different types and colors of limestone. Please click
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It's possible that you might have changed the color of the limestone, or whatever stone it might be, by using the liquid paint remover or even because of the paint that had been on it for a number of years. But, the color change might only be superficial.
If, after determining truly what kind of stone it is and if it's not the color that it's supposed to be, then my suggestion would be to lightly sand the stone in an area that is not all that noticeable, and see if the sanding does remove some of the discoloration. If it does, then you might want to try a palm sander or even a wire wheel attached to a drill to see about removing the additional discoloration. Using either of those methods though, I would still test in an inconspicuous area to see what the result is, and if the result is desirable.
If you need to remove further paint, you might want to try using a heat gun with a respirator for breathing on your face. Using a heat gun would probably speed the removal process up a bit.
Thanks!