Does "advance the active mystery" apply to an AO's final mystery?
Further digging turned up this thread where official rule clarifications from the maker of the game have been gathered.

Turns out it this has been addressed.


  How do the effects "advance/solve the active Mystery" interact with the Final Mystery?
  
  Quote :
  
  
    The Final Mystery is not the active Mystery. As such, “advance the active Mystery” and “solve the active Mystery” effects will not affect the Final Mystery.
  


So, it seems I was correct in how I played it.