The early-access game Shadows of Doubt also has extensive secret-knowledge mechanics which must be carefully managed, with the additional complication that it ideally wants to keep in sync the knowledge of the player and the player character.

I had an opportunity to play it for a few hours. It's not perfect - it didn't always keep up with my deductions, and on one instance it leaked unknown info via the UI - but on the whole it succeeded at a convincing mechanic.