If I remember correctly, the anime staff in an interview for Part 5 were asking for color schemes for the main cast from Araki the author and he advised them to make the colors more varied and not repetitive for characters. Which is how Pink Giorno and was chosen, as the original blue color scheme palette he had in most media looked a bit similar to the dark color palette that Abbacchio and Narancia had.
With that in mind, I think the reason for Jolyne's new color scheme can be explained. As among the main cast of Part 6, there's already another character with a Green / Blue setup... (Foo Fighters).