IIRC there are 5 notes, 2 before the stairs and 3 after.
You've recalled incorrectly. There's 6 notes; 3 before, and 3 after.
Luckily, the 3 before the stairs are pretty hard to miss: your only approach vector to the trap puts them right in your line of sight. The 3 after the stairs are the tricky ones: one is technically plainly visible to your left when Lona wakes up, and one is visible in the next room, but the last requires you to search the northern room before continuing on to talk to Lona, and the graphics in the basement are really muddied together in a way that makes things like corridors and NPCs (and the notes) difficult to see—did anyone else know there's an interactable skeleton in the room where Lona wakes up?
So long as you pick up all six notes though, attempting to interact with Cocona will shortcut to them eating together and then escaping together