This is not the first time this has happened to me, and as before, it still drives me batty.
I booked travel through my employers travel system. When trying to check in for my o-dark-thirty flight in the morning, I discovered that the travel system thought it would be a good idea to cancel the flight sometime between when I checked on it two weeks ago, and today.
I called the "in case of emergency/after hours" number for the travel system, and after about 30ish minutes it got ironed out. No other arrangements were cancelled (rental car and hotel), just the flight. In the past three years, this has happened about 4 times. It happens to the rest of my team as well, and it drives us all nuts. I suppose that is what happens when you choose the lowest bidder for your travel system.