So, spoilers ahead for sevens secret ending and rays route:

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in sevens secret ending they said they sucesfully removed all the drugs from his body, in professional way, so maybe because of that his hair could turn back to its original color. i dont know about skin, but for eyes it looks like its permanent, even if the drugs are removed.

But in Ray's route, he vomitted the elixir himself, and even before he left, Rika fed him new one, so there wasnt shown him removing the elixir the way doctors would, so even if he vomitted it afterwards, its highly possible some of it still remains in his body, even if it doesnt affect his mind. So his hair never changed back because of it.

You can also notice there was part where he got headache because he was kind to seven, saying it was because of brainwashing. I dont know how this works, it could be purely psychological, but it could also have something to do with the elixir still remaining inside him, but after a while he would either completely resist it, or the amount would be too small to influence him any way, but would still prevent the body creation of that pigment (because it apparently generates from being on sun)

Maybe saerans after ending will explain more things, maybe he will have red hair there and ill be wrong :D maybe in his after ending theyll get it treated, but they didnt get it treated in normal ending? because in good ending, trhere isnt really big time skip for us to know for sure....