If I am missing any gears when I put my back wheel on, this is what I do.
If I am missing high gears, for example my gear shifter says my lowest gear is 3rd gear, I know that my lowest gear is actually 1st gear so I take the EX box off the hub while my hub is still in first gear, I then change my shifter to first gear and put it back together. That has always worked for me to get all 14 gears back.
Opposite is the same solution, if my shifter says my highest gear is gear 10, I know that my highest gear really is gear 14, etc.
It took my more time to type this than to remedy it.