Pat, what do you mean it went back to default? Default what? But you should see the yellow, green, and blue LEDs go solid... it might be quick but should be noticeable.
It doesn't really matter when you set those inc/dec settings in the flight controller. But the full calibration process using the PC programs might adjust the values slightly, which is why that part of the wiki suggests setting them after the calculations are all done. When doing the onboard calibration, these values should already be set.
-Max