I have to say, I feel that the mod changing has become a staple part of what makes Thaumcraft so good. Its like different eras of magic with the understanding and technology evolving. It is basically part of the lore of Thaumcraft at this point.
Rediscovery of seals, a lost art last seen centuries ago.
A resurgence in aura node strength causes them to enter high energy states that can drift.
Major upheaval in golem research occurs due to the resurgence and growth of auras granting them sentience. Many researchers died before they were contained. New research will be needed on the interaction of auras and golems.