Kryptonians get their power from Earth's yellow sun, however when they are on a planet that has a red sun, they are essentially human.
Kryptonite was irradiated by Krypton's explosion, it's not affected by the radiation from the different suns. Green Kryptonite is deadly to Kryptonians due to the radiation it absorbed from the explosion, it doesn't remove their powers, it simply poisons them.
So with that said, if a Kryptonian were on Earth, full powers and everything, and the Earth's yellow sun was turned into a red sun, thus gradually 'turning' the Kryptonians into humans(I know they aren't transformed into humans, but they more or less share the same physiological attributes), would these Kryptonians still be affected by Kryptonite?