The map's architecture

[Adny]

Hang on...didn't he consume the potion in the room where he wrote the note to himself?

There are similar trails in the dungeon/choir to the ones in the intro map, which now that I think about it could be for the prisoners. Anyways, it still doesn't explain why there is a note from his journal in the room before the inner Sanctum. I doubt Alexander would spread the notes around, so I'm pretty sure that from notes/flashbacks, Daniel had previous access to all the areas he visited from the intro all the way to the sanctum; so my point still stands: why is everything locked and unsolved? Why does Agrippa greet you like you've never met before? Although it's a large castle, there's a pretty linear line from intro to the sanctum.

tl;dr - I am confuz