I'm already impressed that they're admitting there was a flaw and are offering to replace it. It shouldn't be a problem for pros. Of course, the backsplash/counter joint will have to be caulked again.

I'm assuming this is a manmade quartzite material such as Zodiaq. In that case, there is a limited warranty of a colour match from Dupont, which should apply to any replacement as well. If you have a different product, check for the relevant warranties.

Dupont Zodiaq warranty (in part):

"Color Variation Within an Installation: Since DuPont Zodiaq® is made from natural quartz, variations in the color, size, shape and pattern of distribution of the natural stone (quartz), and the tone of the background, are inherent and unique characteristics to be expected with this product. If the natural variation is visible in an installation from a distance of 7 feet or greater with uniform lighting (no spot lights or high intensity lighting) it will be considered to be a material defect and covered by this warranty, but you must report it within ninety (90) days of installation. If the color variation is not visible from 7 feet or if it is not reported within ninety (90) days of installation, it will be considered to be a normal variation and not covered by this warranty."