I never realized that the episode "Holiday Hi-Jynx" was re-edited in 2012, and this new edit aired in Japan on 23 December 2012.
Basically they spent time to edit Jynx's face to purple and her forearms to white.
I'm making a wild guess that they plan to air this episode internationally in the future, otherwise the edit would not have been required.
(If it's Japan only, there's totally no need of doing the edits)
As far as I'm concerned, UK keeps airing the non-edited black Jynx version nearly every Christmas.
Anyway, I actually feel that the Game Freak staff liked Jynx a lot, even with the controversies.
It's kind of funny how they released the first official Jynx plush in April 2014. (I lived long enough to buy myself a legit Jynx plush!)
They also released a matching rubber keyring not long ago. (Oh, I bought that too)
In the episode "Pokemon The Origins", you can see 4 Jynx in the photos of the Champion room. Strangely, they are black faced.
(You can find the pictures in the Jynx Club database.
Jynx's Japanese name is actually trademarked, along with most other Mega Pokemon. (They spent money doing it!!)
And they spent money editing the episode Holiday Hi-Jynx despite this episode was 15 years old when they aired the new version.
In the Team Rocket Empire movement during Pokemon Best Wishes, Jesse's voice actress states that Jesse's favourite episode is supposed to be Holiday Hi-Jynx.