Kyran marked Shiloh and Uilleam before creating an automa part to replace their missing limbs. He did this because they could become a liability if they were to encounter another one of the tower's challenges or an ambush from another group.
Then again, now that the tower recognizes Kyran's identity, he might be able to effortlessly navigate through the tower and its challenges and even transfer to other levels at will. He would not do that, however, because he was sure the tower would only allow him to do that and not the people with him.
After resolving the matter with Shiloh and Uilleam, Kyran took them and returned with the others.
Cyneah, who already sensed their arrival could not help but wear a perplexed expression.
"I've marked them. They will not pose a threat for now."
"Yes, I can see that," Cyneah replied, looking at Shiloh and Uilleam's lights, which were now mixed with a black hole-like mark in the middle.