Sure, this has happened. And it's easy. You send them a note (or even better, call the PD) and explain the situation. Apologize profusely, resign your position. Do it as early as possible, so they can hire someone new / fix the schedule. Since there's no match, there's no waiver needed.
Will you be able to get a spot again in the future? Hard to tell -- depends upon how competitive you are, and how non-competitive the fellowship is. If you're polite enough with the program and they liked you, they might consider you for the future -- although I wouldn't count on this.