No problem.
Sometimes some policies that might get spoken of, or misconstrued, are a function of- how should I say this politely- "lowest common denominator". 99% of users are going to use/install something properly, and 1% will screw it up no matter what.
For example, using a battery charger when flashing. We catch some flack from customers from time to time over being strict about this. But the truth of the matter, is that a few guys have cooked modules by programming with low battery voltage. This will happen when programming with our product, SCT, Ford's own IDS, or any reprogramming device. Bad batteries, leaving the truck sitting with the headlights on, etc, then getting mad at us despite the "I told you so" at the beginning. A healthy truck with a healthy set of batteries won't have any issues, but we have no idea of knowing what the electrical condition of your truck is when providing tech support.
On the 6.4L, it is possible to get the truck in a bit of an electronic "jam" by attempting to run/drive it with hardware disconnected when switching between flash devices. Therefore, our general recommendation is to hook it back up. It's not entirely necessary, but once again we can't predict what the customer will do over the phone that may lead to problems.
If anyone was mistakenly told you needed to re-install hardware on the 6.7L, my apologies- just sent out an email to clear that up. Just keep in mind that a large portion of our instructions exist for the same reason that there is an obnoxious warning on a cup of coffee from McDonald's--- it exists because it's been screwed up in the past.