I don't see why not, it should only touch empty data, so it won't break a game, no matter how many times you run it.
I would like to know if running in "trucha" mode also scrubs a disk? This program is becoming more advanced, but also more complex, and that isn't a good thing. Either the program should do one thing, and do it well, or the interface needs to be re-designed to make the options more obvious and day to day operations simpler.
Perhaps a menu bar with a preferences/settings pane? All the options could be set there. Perhaps a preference to toggle "advanced mode" on and off?
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