I'm guessing because she is the only real villainess in Batman's rogues gallery, and they wanted to keep her that way instead of having another antiheroine like Catwoman.
I think that's what it was, too, since she started the feeding people to plants thing right when Harley was shifting from "sympathetic likeable villain" to antiheroine. This was also when Roxy Rocket was finally brought into the main DCU, and the new Ventriloquist was introduced. And now, Battle for the Cowl has brought back Jane Doe.
Not saying it's a good idea, and it looks like they may have changed their minds recently.
Well, if she's going to be teamed with Selina and Harley, she can't be chopping people up. Doing psychotic monsterous things to people suits Jane Doe better, anyway, I think. Maybe the animated series and Gotham Girls has changed the public perception of Ivy more than they realized, and she's too identified with Harley and, to a lesser extent, Selina, now.