ToME: the Tales of Maj'Eyal

I've done this quest with several characters, so I understand what is required to normally get through this quest. I have a number of unequipped yellow artifacts in my inventory.
In my current playthrough I'm pretty sure that I did complete this quest. However, I left one of the earlier dungeons (Daikara I think) because I was losing the boss fight. When I went back to the surface, it regenerated the map - it was all fog of war again. Later when I triggered the Storming the city quest and needed access to the magic user's town, I noticed the passage to it was missing. The apprentice was on the map, but whenever I would talk to him the only dialogue option I have is "Sorry I have to go!"

The bug here is that something caused your world file to get corrupted and thus it was regenerated. Since you've already done the Angolwen access quest, your quest flag states such and the Apprentice mage will not offer the quest for you again.

If you wish to do the quest again, you must manually delete the quest from the character via save editing or devmode. I can also do this for you if you're not fond of fiddling with the files yourself (Moasseman#7143 on ToME discord)

Ps. Did you have your Rod of Recall configured to take you to the Sher'tul fortress?