The truth was that Kyran did not mine the spirit stones. Instead, he assigned several puppets he acquired to do it.
As for the Armakeans guarding the mines, they were either knights or high-ranked officers who were all bound to Aran by the pact. After being released, they were similarly confused and lost at what to do. But because of the knights' discipline and the officers' dignity, they still diligently guarded the mines.
When Kyran arrived, they were initially wary.
Not wanting to start an unnecessary fight, Kyran called Filren and had him speak with the knights. He also summoned Breira and asked to take them back to their temporary base.
He then ordered the puppets to mine while assigning two automatons to supervise them. After that, he returned to the Magical Beast Community to check on the three magical beasts, who were busy dealing with the situation.