Having the same issue, will post back if I ever figure it out.
I'm using two external Mini-Display-Port to DVI adapters. I've had luck restoring visibility by swapping thunderbolt ports. Not only is this a pain, but it resets all window positions.
And RE: Joseph's suggestion. I do not believe either of us consider not sleeping the PC a valid solution here.
"Detect Displays" does not wake display using SwitchResX. Powering off/on display does not wake display (when it comes back on, it immediately returns to sleep detecting no signal).
Using gfxCardStatus to force switch from discrete, to integrated, and back to discrete does not wake display.
Removing and reinserting cable from thunderbolt port does not wake display; although, the remaining integrated and tertiary displays that do work flash blue while "removing" the display from the display set, they also do this upon reinserting cable.
This issue seems to be unrelated to system sleep, I have system sleep disabled when powered by AC.
I'm currently trying to include or exclude the following correlations:
Of the two thunderbolt ports, is there a specific problem port? I know I've had this problem on both displays, and only one at a time, is this related to a specific problem port that's a recurring issue?
This issue seems only to recur when the display is asleep for an extended period. I cannot seem to reproduce the issue by simply sleeping displays.
My deterministic mindset is steering me toward the observation that the technology controlling a "switch" between Thunderbolt and Legacy DisplayPort is not properly passing signal from the display adapter through to the display.
DDC is working but TMDS is not?
Someone who knows more about Apple's Thunderbolt implementation might suggest additional troubleshooting steps, though I'm leaning toward a hardware issue that may or may not be fixable through firmware upgrade.