There’s not a whole lot more to it than that, but I’ll provide illustrations.

Knuckles turns green (and comically overpowered) because of chaos emerald energy something or other, and because Penders wanted to make his mark on the character he’d come to regard as his property. Place your bets now as to what the payoff will be for this setup.

No characters ever comment on his color change again, so if you’re just dropping in and it’s not one of the issues where they mention that he’s “Chaos Knuckles” (and it probably isn’t), Knuckles is just green and insanely powerful for no discernable reason.

Knuckles dies at some point and is about to ascend to godhood, but comes back to life because they made Penders retcon it. When he returns, he says his Chaos power is gone. Neither him nor anybody else comment on the fact that he’s red now, and it’s never brought up again. Oh, and the payoff was nothing, he was just a green super Knuckles for a while and it didn’t go anywhere.

And I can’t even begin to overstate how weird Penders got with his OC echidnas (or later on, the legally distinct echyd’nyas). It started at a weird place and it went to a really weird place when he started making the comics on his own.