After the battle ended, Max began to work on the numbers to see what sort of progress that he was actually making. He couldn't be sure of the end goal of the System Nanobots, but he could say for certain that he hadn't become a Greater Energy Being.
The conversion rate on the energy was terrible, but the remaining energy was sent out as various types of heat, light and radiation, not the stabilized energy that could be used to rebuild the Lesser Energy Beings.
While tearing it apart with the Disintegrator completely dispersed the energy and broke its bonds, this was enough to convert it into something else that hopefully could never be used to rebuild another enemy.
That was precisely what they had been hoping for. SO, even if a part of it that couldn't be converted was being used to make a new energy being in the boundary between layers, there were still going to be a significant net negative number of them wandering around the universe and causing trouble.
