The map's architecture

[cantremember]

When he enters the ransacked guest room he says something like "my journals, what would they want with my journals" so I'm thinking his journals could have been scattered around by the gatherers.

He has been to the orb chamber before, but probably not right before he took the amnesia potion, but when he was still gathering bodies for vitae and such. Alexander could have stolen Daniel's orb and lock himself when Daniel was anywhere. The elevator still worked, the refinery wasn't blocked by red sludge yet, the archives wasn't flooded with water, Alexander had the keys to pass through the prison and he didn't have to go through the sewers the first time he went to the inner sanctum.

The only thing I find a little strange is that he never saw Agrippa (perhaps he entered the nave via the Chancel, and didn't walk further than the two doors to the torture rooms, assuming Agrippa was just a dead man, he can't speak to you telepathically until you pull the switch).

Also why Daniel would hide a key to the elevator machine room behind a painting in his room.