The writer of that storyline, Ty Templeton, said this on Toonzone.
The Ivy Clone was substituted whenever you want her to be, but in my mind, it was somewhere between the last issue of Gotham Adventures and the first issue of the New Batman Adventures. (The Harley /Ivy mini is therefore, "safe" and is STILL about the original Ivy, since it was written and drawn years ago.)
I had in mind that it was not the real Ivy back in Batman Adventures (vol2), issue one, when she's stabbed in Arkham and survives it. That was the point of the stabbing scene.
In the recent issue, on the last page, we back dated Pamela's look to an earlier BTAS design to suggest she's no longer super-powered, and has reverted back to her more human form in retirement... (I figure the toxins and serums would eventually work their way out of her system and she'd revert to an earlier form.) Also, it was a much quicker shorthand in a story that's only four pages long, to distinguish which Ivy was which.
But I wouldn't retcon away two seasons worth of appearances by Ivy. That would be rude. So, in my mind, the plant monster version shows up first in Batman Adventures (vol2) #1, when Dan and I started writing it... Every other Ivy story is still intact.
Or...you can believe it's been a clone since season two. That's part of the fun of the ending.