I don't necessarily have to reset the Arduino completely it would be sufficient just to have the counter be zero at the point that my magnet switch is closed along with the motor to immediately pause for a second or 1.5 seconds. what some responders are not understanding and don't get me wrong i am not blaming them. don't see this as a shortcut I see this as a protective measure. say your engine rpm is up around 10000 and you shift thru the neutral position into reverse from forward. That would be absolutely dangerous. and the possibility someone at the controls could do something like this accidently is completely avoided by the resetting the program at this spot in the program. the fact that it is also fixing the problem of missed steps is just an added benefit in my opinion. Its true my coding hasten advanced very far and I've been working on this for a couple of years . but the throttle control code works and im just tying to true up the stepper motor and sync it to the throttle servo this seems the most eloquent way so far. a more eloquent way wouldn't be to to ignore the need for a safety stop in this point of the program.