When repootting trees, especially in a period that is not idealfor transplanting, I always work on the assumption that part of the canopy might die. Which is why I think waiting for the pant to establish, and then make plans, is a better route to take.
You never know whether die-back occurs. But Junipers have fairly dedicated links between roots and branches. Cutting a very big root could cause dieback in the canopy when plants are weak to compensate for the root.