It seems like that some data is persistent, even if you load an earlier savefile or start a new game. This comes up with Lyx's quest to read minds, with the mind-reading counter increased despite having loaded a save prior to the quest. Exploration points also have their Remember directions retained on a fresh playthrough.
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Yeah, the first is a quirk of Ren;py (the underlying SDK) and the latter was to stop people complaining :P
Basically, the "Hidden Voices" skill has to use an extra "instance" of the game, so that players can use it without interrupting ongoing conversations or events. Unfortunately, the way Ren'py is designed, you can't pass standard variables across instances - you can only pass persistent variables. Hopefully this will change before CK is finished so I can redo the code.
As for remembering the exploration directions, that was because when the EXPLORE system was introduced it got a lot of complaints from people who didn't want to have to work for their content. So I made the events mostly appear automatically and the "remember" function permanent. The latter will be removed from the final build.
Hope that clears everything up! :)
As I understand it, there has been a revision of Renpy that was a released - adding support for Python 3. Would updating CK to that version allow for correcting the quirk, among whatever else that plagues developers?
Anyhow, thanks for the response. It is good to see developers address bugs and commentaries, it makes me feel like reporting issues as I find them. Hopefully, I will (not) find issues, but will keep an eye out.