Base Running Error?

[my3sons]

Friend of mine was telling me about this situation. Tournement game using MLB rules. R1 and R2. The game goes into a 1-1/2 hour rain delay. When the game resumes the runner that was on first is now on second and the runner that was on second is now on first. The umpires nor the teams realize the mistake. The umpires put the ball in play and the pitcher throws a pitch. The defensive coach now realizes that the runners are in the wrong order and he brings this to the attention of the umpires. They rule that since a pitch has been made that they are leaving the runners where they are. Two questions. First how would you have ruled on this and second what would you have done if the defensive coach had appealed this before the pitch was made. One thing I learned from all this is to write down everything when I have a rain delay including the numbers of the runners and which base they are on along with the other info I would normally write down.