I may have discovered a (duct tape) fix! If you have bluetooth headphones connected to your phone, while still utilizing Sync for the call it doesn't disconnect!
I was having this same problem with a 2017 Ford Fusion and a brand new iPhone 7. My music/audio connection was fine, but phone calls would drop and reconnect ever 1-5 minutes.
I was traveling in my car talking on the phone for over 15 minutes yesterday and had my bluetooth headphones (Beats) connected to my phone, as well as Sync. I was utilizing Sync to talk on the phone and it DIDN'T DISCONNECT ONCE! The following day, I started a phone call via Sync, without my bluetooth headphones on, and it disconnected within the first 2 minutes of the call. I then turned on and connected my bluetooth headphones to my iPhone, but continued to utilize Sync, and it didn't disconnect at all for the remainder of the 10 minute call. Again, EVERY OTHER TIME I've done would've disconnected multiple times during a 10 minute phone conversation.
While some might say if you have to have your bluetooth headphones connected, why not just use those? Personally, it's much less comfortable to have the headphones in when you're driving. Also, I am much more satisfied with the mere burden of turning on the headphones, then having to deal with the stupid disconnect every 2 minutes! And for those that have this issue, you know that when it disconnects and you then select "Speaker" or "iPhone" from the bottom menu, shortly thereafter it will automatically connect back to Sync! So you have to then turn your bluetooth radio button off.
I will continue to test this out and update if it doesn't hold true.