Just exploring another possibility here, thinking outside the box.
What if everything that happened in the Panzer trilogy was the plan of a select group of the Ancients? Sestren, the Towers, the heresy dragon, Azel, the destruction of the Towers, all of it. Even the end of the Ancient Age. These entities and events seem somewhat seperate, yet the different entities involved could have been given unique purposes and missions deliberately by the same force.
Take for example Azel. We know that Azel was stolen, but we have no proof that she was given a new purpose by the rebels. What if she was designed to assist the heresy dragon, who in turn was actually part of the will of the Ancients. A dragon intended to free the world from the will of the Ancients after a certain period of time, set by the Ancients themselves.
Indeed, it is always assumed that Sestren was the ultimate controller of the “delicate balance” that the Ancients created. But what if the dragon was another part of this balance too, yet Sestren - being only programmed to protect the Towers - considered the heresy dragon to be a rebel. Yet, this too may have been part of the plan; the Ancients may have known that Sestren would ultimately have to be “ended” by the dragon, once the task of the Towers/Sestren was complete. If this was the case, Sestren would have been created with a set lifespan in mind.
Perhaps the Ancients did plan to return, once the Towers had achieved their goal and the dragon had terminated them. However, by the time Abadd tried to revive them, their hibernation chambers had ultimately failed due to a malfunction (perhaps caused in an accident during the end of the Ancient Age or the Great Fall).
I admit there are a number of weaknesses in this theory, but lets discuss why this could or couldn’t be the case. Could the “heresy” dragon have been part of the Ancient plan all along?