Dr. Atkins repeatedly challenged anyone to bring forward a case where low carbing caused damage to healthy kidneys. No ever did and no one ever has since his death. So I think you can relax on that score. People have been saying that for years and it's still not true, no matter how many times they say it.

If it helps, I've been on LC for over 6 years and have no kidney stone problems.

Keep drinking several litres of water daily as that helps flush out the by-products of the fat you are burning, and protects against the formation of kidney stones. Another reason why LCing is good.