As long as you've saved your tournament, you can exit, restart, reboot, whatever, start up the TD again, load the tournament, and you should be exactly where you left off. I always recommend you enable Auto-save, so you can always get back to exactly (or very close to) where you left off. In a future version, once the code is ported to a new framework, auto-save will be the default.
Game over only occurs if the tournament has already started and there is 1 or 0 players left in the tournament. Were players suddenly busted out when you loaded the tournament again?