Lobotomies

In the video explaining the history of Clonus, they say that they originally had trouble with the clones, then realized they could lobotomize them to keep them docile.

Meanwhile, in the present, they keep them all in a community sheltered from the rest of the world, fully conscious and aware. Then after the escape, they lobotomize the girlfriend of the one who escaped, to help lure him back. This raises the question, why did they stop lobotomizing them all in the first place? Surely it would be easier/cheaper to keep a bunch of lobotomized bodies in beds with growing organs anyways, not to mention it minimizes the threat of escape, which it looks like ended up undoing them.