I think I experienced something similar at a gig Saturday night. I say similar, because in my case, I was un-docked, and only some controls were affected. I did not get any indication that sync had been lost, and, since most controls were working, I'm guessing the system didn't "think" it had lost sync. Switching screens or waiting a short time would get the controls back.
My DL-1608 has a 30-pin connector, and I use all devices with Lightning ports now. All are on Master Fader 4, and my devices (iPad Air 2, iPhone 6s, iPhone 5 docked with lightning-to-30-pin adapter) are running iOS 9.3.1. I did have two performers using Master Fader 4 on iPhones as well to run their in-ear mixes. I do not know what version of iOS they were on. I have the DL1608 set to fixed IP now, and am using a 5GHz router to stay clear of most of the rest of the usual 2.4GHz WiFi traffic. I don't think that either of the performers noticed control issues, but had issues with both the iPad and the iPhone6s.