If you pull your flywheel, or swap engines, or rebuild your engine, remove it, etc., you will need to do this procedure to your vehicle. It does not affect your tune at all, it's to align how the computer finds #1 cylinder is how it was explained to me.
Two ways to get this done. First is to go to Ford and ask for it specifically. Second way is to use a snap on scanner, has to be within the last year's model(2014), as it has it on there as well. So now even local spots can do it.
I'm looking at getting one of these scan tools, which made my snap on guy very excited, so that I can do this reset easily when I put a coyote engine in or do a clutch or flexplate on one. They even recommend doing this when installing a Circle D converter.
Just an fyi.