Just an update for anyone who runs into the issue with their iPhone not connecting to the Mavic Pro RC/AC with either cable into either port in the remote.
I had just experienced this issue after many flying sessions with no problems connecting my iPhone 6S Plus to my Mavic Pro, suddenly, it would no longer connect to either port of the R/C. Tried all of the suggestions I could find, using different charge cords (I have several) and both ports, startup sequences, updating the firmware, IOS on the phone, etc. Nothing was working. I COULD connect to my iPad with no problem, and I COULD connect to the Aircraft using wifi with my iPhone.
What I did notice though as I was trying every charge cord I could find was that some of the cords would not even connect to my phone. I had this problem a year or so back, and solved it by cleaning out the charge port. This time, cleaning the port became a little more challenging, as I used a plastic dental pick and poked inside the port trying to dig out any debris, lint, etc. It took me several tries, eventually, I took a tissue and packed it into the port gently a few times with the dental pick and then blew the port out with some compressed air. Once I got the port completely clean and working with all of my charge cords again, I connected phone up to the Mavic R/C as normal and everything is up and working again. So long story short, if you carry your phone around in your pocket regularly as I do, and you run into connection issues, try to do a thorough cleaning of the charge port. This may just solve the issue for you.