The flash connection is relatively new, but it has happened on three shoots now, I shoot some real estate and have 600-EX-RT's inside the property and control them from outside, with the ST-E3-RT this is effortless and 100% reliable, however with the YN-E3-RT it is not so and when they do stop talking I have to take the YN off the camera and walk it back into the property, often the same room, to get it to reconnect.
The good thing Yn actually does respond to requests, and this sounds something they cannot ignore. How long do you have to stop shooting for the controller to work again, is it a thermal issue? Do these problems only happen on your legacy pre-2012 1d3, or also on new bodies that are supposed to support rt flashes?
I believe many will never have an issue with the YN, I probably work them harder and longer than most would and the reliability seems to drop off as shoot time goes up. For pre 2012 cameras and non critical/short term use they are still a way better buy than the ST-E3-RT, for longer shoots or with post 2012 cameras just get the Canon.
... unless you need the af assist, doh. I do hope Yn gets this fixed with a fw update (bless them for the option!), I guess they are interested in getting this right since it looks like this is to jumpstart their whole rt flash line.