Then people will think that's the time remaining to finish the final mission, and they will think that when it reaches zero, they fail the quest and have to start over. So, they will restart their console and post on the forums about the bug.
*sigh* If the timer has shining red text that says "Time until you can select [Yes] / [No] on the pop-up (Note: Time countdown is not time countdown for final quest, DO NOT RESTART THE DAMN CONSOLE/PC!!!!)" right next to it?
Not really in the mood for nitpicking.
* Have it non clickable for 30 seconds with some elevator music rolling in the background.
* Have a countdown timer next to it to indicate that game has NOT frozen.
* Have a message right next to the timer stating it's not the countdown for the game but just the countdown for the pop-up.
Problems officer?