Two of our local dealers scan every vehicle as it comes in, regardless of why it's there. However, not all of the dealers do that. I'm not sure what that initial scan is capturing, but its possible that ignition cycles or some other status may be captured via the OBD tool. If you are truly worried, rolling back to your stock won't hurt but that's going to reset your cycle count. However, it may give them one less reason to poke around.