I had a very similar issue. I updated yesterday to the new 10.9.3 with the support for 4K monitors (which I do NOT have) and it broke my Thunderbolt display.
Here's what happened, I updated and after the reboot, my Thunderbolt was "active" meaning the screen was on and peripherals worked that were attached, but I only had a black screen. The mouse would show up on the screen as well. I checked brightness and resolution, but nothing showed up. When I changed the rotation, the screen would flash on (showing my desktop background) and then flash off.
So the solution above by cristobal.sandoval worked, but the directions he gave are not exactly how it worked for me. First, I have a Mid 2012 15" MacBook Pro with Retina Display. So I powered off and the did what the post above says, I held down Shift-Alt-Cmd and pressed the power button. No status change on the power cord's LED occurred. It booted up and my Thunderbolt was gray now, instead of black as it was.
I attempted it again but no change.
Then I just went straight for part two. From a completely powered off state, I pressed Alt-Cmd-R-P-Power and held it down until I heard the Mac Chime two times. It chimed once and then went black for a few seconds and then chimed again. I released the buttons and both my monitors are working again as before the update. Just wanted to post a little extra detail in case other people are experiencing the same issue. What a weird bug in an update. I feel sorry for the people who don't know how to fix problems themselves and will be stuck with this bug until Apple releases a new update.