I download the updated version before removing the old one (don't know if this has anything to do with it) but my scene unlocks are still there. I don't remember if gear is, I usually reset before I start so i have something to do while checking out what is new.
Sorry for the late reply! Like Ren says, gallery progress will carry over, but right now character progress is still tied to specific versions to simplify identifying and fixing bugs. You can purchase scenes from Mr. Black in the Void Slums, but as mentioned gallery progress should carry over.
