I've been keeping up with everyone's responses since I posted, and I have some adds and observations:
I think this is a Sync problem over an Apple problem. I had it happen this weekend again, and it was with my boyfriend's iPhone 6 hooked up to my car on a road trip. We completely lost the use of the AUX and phone functions, same as what usually happens.
Difference this time is it's been 4 days now and the functionality hasnt returned in my Escape to use AUX or phone functions at all. When I hit AUX it goes back to FM1.
My car says it's on the most up to date version of Sybc as well. So I think it may be a Ford Sync issue where either it isn't compatible with whatever the newest iOS is, or Sync just need a major update for Apple period.
I read a ton of Ford discussions over the weekend as well, and many people are having the same problem - intermittent Bluetooth dropout, AUX functions completely stopping and phone functions completely stopping while using Apple products in their Fords. Some said they've been to the dealer 3 times and it still happens after a reset. Many people say they pull fuse 3 in their cars, or disconnect and reconnect their car battery, and it fixes it temporarily. I tried pulling fuse 3 (the Sync fuse) over the weekend, and it didn't work for me. It has worked in the past.
So those are my 2 cents about the whole thing. I'm stuck listening to radio and CDs right now until I can take my Escape in. Thumbs down. I have the service plan where it's $100 to work on anything on my car electrical or whatnot and have it fixed, but I'm hoping when I can take it in for an oil change I can sweet talk the guys into checking it out for me. I cannot even access the menu options anymore to do a Sync system master reset. It only stays on AM/FM or CD.
I'll update if I go to the dealer. :-)
~Monica