I just did this part - well after i got the tenebrium skill, went all around, cleared half the map and went through his office, took the two stones there and emerged back in the immaculate chapel in Silverglen. (didnt use them though)
Did the spiders...etc, etc. - then went to do the trial.
Used the stone there to heal myself from Rot.
Everything works fine - but i followed him to the portal when he ran and had the fight right there when he came back with reinforcements.