The protest involves a play that had a significant impact on the outcome of the game. In such cases, and there haven't been many at the MLB level, play is resumed from the point of contention. What happens to the stats from innings 6 to 14? Would they all be wiped from the books, or just the winning and losing pitcher stat?
http://www.retrosheet.org/protests.htm
This is about as complete a list of resumed games after protest as you'll find. Most of them had to do with rain or curfew delays that simply had the games start up again. As best I can tell, this might be the first game in MLB history where more than half of the innings played could be negated if it is to be resumed from the point of protest.