As BTAS shifted into the New Batman Adventures, they updated several of their character designs to fit the more uniform style established in Superman: the Animated Series which would become more or less the standard all the way through to JLU.
Several of the changes go unexplained, The Penguin going from a more Danny Devito inspired look to a regular person, for example, isn’t really explained. Ditto the Joker loosing his lips and getting black eyes.
They do explain the change from Selina Kyle being blonde to brunette, and Poison Ivy from caucasian to having green/white skin, however. Cosmetic changes, but with DRAMA.
With Selina, we get a storyline about why she and Bruce are on the outs in TNBA, where it turned out that she actually dyed her hair, but stopped after she learned her brand was created a woman running an illegal animal testing lab.
The falling out occurred when, after Batman showed up to rescue the billionaire from Selina (and to inform her that her activities had been revealed to the press), the woman thought that it would be a good idea to kick one of the cats on the way out. This results in Selina clawing up her face, an act so horrible that this permanently ends the Selina/Bruce friendship apparently.
With Ivy though, the tie-in comics explanation actually is more widely tied into the changes she’d undergone in both BTAS, TNBA and the comics themselves. See, while Pamela started as a regular person but her continual self-experimentation first leads to her being immune to all poisons and toxins, then her seemingly turned into an actual plant-person like the ones she’d frequently been creating in vats in both shows.
Note my use of the word “seemingly“, it’s eventually revealed in the story the Flower Girl, that when Pam left Gotham for South America in the episode House and Garden, she never actually came back… And instead sent an unknowing plant duplicate back to Gotham to keep Harley company as she’s the only human connection Pam has.
So yeah, the reason for Ivy’s pigment change (and over-reliance in plantfolk) is because that wasn’t actually Ivy, as she’d gone to hang out with pre-Swamp Thing Alec Hammond in Louisana instead. Kind of makes sense that she’d make a friend for Harley though, this photo album was one of the few things Pam managed to save before fleeing in her final episode.