Think there's a little confusion here. The manual shifter is for emergency use, in case the ES fails. But when you use the manual shifter, it confuses the angle sensor and sets off an error code. All you need to do to reset it is turn the key off and on again. Of course if you still have a problem (the original one), your N will probably still be flashing. If it was an intermittent type thing, your machine will work normally until an error occurs again. The self diagnostics store up to two problems in the ES memory, which can be read at a later time. Just be sure to keep in mind that one of those codes will be an angle sensor caused by the manual shifter. If you are having a dealer fix it, be sure to tell them you used the manual shifter so they don't replace angle sensor needlessly. If there is a problem, usually it's best to erase the memory and test ride until it occurs, then read the diagnostics immediately, so the results are not confused by use of the manual shifter. There is an initialization procedure, but you shouldn't have to do it unless you actually replace the angle sensor, carb (TPS), or ECM.