I ended taking it to an apple store for support and they gave me no help. It was the first time I have been throughly angry by apple support. I would have expected more from them.
They claimed that removing the stand is a non-standard use of the montior which invalidates the warranty and wanted to charge me $250 to try and fix the problem. They would have needed the display for 3 - 5 days and couldn't explain to me how they were actually going to fix it....
Awful customer service imo.
So I fixed it myself. I found this explaination on ifixit of how to take apart the screen
http://www.ifixit.com/Teardown/Apple+Thunderbolt+Display+Teardown/6525/1
I went to home depot and purchase two heavy duty suction cups (these: http://www.homedepot.com/p/QEP-4-7-8-in-Suction-Cup-for-Handling-Large-Non-Porous-Tile-75000Q/100119050#.UZG_7CtAR90)
Within 10 mins I had the display opened. I was then able to fit the stand through the opening in the back of the display and screw in two screws to secure the stand. (I screwed them in from the inside of the display.
Then I could relase the latch and move the flange using the stand (since it was attached with the two screws)
The whole process from opening the display to closing it back up took 20 mins. This should have been incredibly easy for the Apple store to do I am sure seeing as how they open these types of screens (iMac screens work the same way) often I would think.
Anyways, hope this helps someon else that is stuck in the same place I was.
Note: that opening the display voids your warranty (howver, Apple claims that taking the stand off of mine voided my warranty already so.....)