Sigh. Never mind. Pushed forward, in many cases by using the pen to fill in the answer, quitting the level, and going back into the level, which reset the pen hint. But Level 32 is literally broken: there's no way to input a number!
There's so much here that seems like a good idea, but if nothing else I feel like it's badly in need of playtesters who can say "this clue was clear; this one was too vague for me to get".