I am having a similar issue. Here's what I have:
2016 Expedition w/Sync 3
iPhone 6s+
90% of the time it works very well. There has been about a dozen cases since I bought the truck last fall where the phone disconnects from Sync 3. Not just bluetooth mind you, also USB! I cannot connect to it with either, so no phone calls or media. The only way to fix it is to turn off the ignition and then restart about a minute later. Words fail me. My enthusiasm about the system is ruined by these very frustrating experiences.