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I mostly buy older games on GOG, so none of my other games have in-game achievements. Since this does, I was wondering if installing the new version would allow me to maintain what I've unlocked in the old version.
This question / problem has been solved by Amy_Strykeimage
Achievements are stored with the game settings.
The game settings are saved as a file called persistent.
At least on Linux, persistent is stored in ~/.renpy/LongLiveTheQueen/
(I believe on Windows7 it's in /Users/<user>/AppData/roaming/renpy/LongLiveTheQueen/)

As long as this file still exists, your settings (and achievements) will remain intact through updates.
Post edited March 16, 2015 by Amy_Stryke
Thanks for the info.