There are many question aasking what happens if you accidentally kill Reshiram/Zekrom, but I have yet to see a question asking what would happen if it kills you. Would you transport back to the pokecenter inside N's Castle? What if you talk to the warp guy and leave from there?
If Reshiram/Zekrom defeats your team, you will be transported to the Pokémon Center that is inside of N's Castle so that you can go back up to try again.
