Seeing as the flags are stored in the RAM and cleared and loaded each time you start the game, are you looking for a massive script that clears the flags? If so, I wrote one at one point, but I have no idea where I put it. In which case, you could just write your own. If you want to reset the events, you also need to reset the vars too. That would be the best way to go. However, remember that some flags, like the pokedex enabler, shouldn't be cleared.