I run a mid 2012 MacBook Pro as my main system. It drives two Apple Thunderbolt Monitors. Prior to my clean install of OSX 10.9 Mavericks, I worked with both monitors connected (as an expanded desktop) without issue. Now it regularly ignores the second monitor after the displays go to sleep.
Similar issue here. I have a 15" Macbook (early 2011) and a single thunderbolt display. Often, when the mac wakes from sleep my thunderbolt display does not connect.
I found that unplugging the thunderbolt cable and reconnecting it gets the display recognized again. Not ideal but at least better than a reboot.