Jay is actually down an eye after the events of Skybound. (After the time rewind, he lost it during the Dark Island Trilogy)
He was worried about what questions he'd have to answer if he continued going around with an eye patch, so the ninja all pitched in to research a place to get him a prosthesis that would also not reveal anything to the media. Then they all pitched in to buy him one that matched the eye he still had, and they succeeded in avoiding any awkward questions from the media.
He started being okay with missing an eye after a while, and it became a bit that for his birthday, at least two or three of the ninja would get him a new eye prosthetic that ranged from natural eye colours to crazy iris and pupil colours, like one with a yellow iris, one with a white pupil, and even one that was just straight-up glittery. (His favourite + most comfortable one is the one with the yellow iris (it matches his outfit)) He didn't wear an eye that matched his own after he started amassing a collection.
Extra: his eyes glow when he uses his powers, but now, only his actual eye glows, and the prosthesis doesn't.
Extra 2: He went into the merge with an unnaturally-coloured prosthesis, but when the Administration kidnapped him, they switched it for a normal one and incinerated the one he had. When Nya saw him for the first time post-merge, she had to do a double take because the last time he wore an eye with his natural eye colour was back when he was still insecure about it.
Man really can't keep that eye to save his life, huh....