Since your settings and game saves and others are stored somewhere in your $HOME directory, reinstalling a program won't fix that.
I think you have to find that counter or PID file or something like this and reset it manually.
As I found here (http://www.chewbranca.com/img/flare-game/), settings are stored in one of these places:
$XDG_CONFIG_HOME/flare
$HOME/.config/flare
./config