My Mac is connected to two Apple Thunderbolt Displays. The first monitor works without flaw. The second however will randomly turn off its screen 3 to 4 times a day. A quick but annoying fix is to un-plug and re-plugin the Thunderbolt connector. I have them daisy chained from my Mac Pro to the first display, then from the first to the second display. Devices such as Thunderbolt hard drives and my keyboard still work through the second display even when the screen is off. When I swap the displays, the one on the end of the chain will always turn off.
Running OS X 10.11.3, Mac Pro (Late 2013), Thunderbolt Display Model Number: MC914