yeah, I always do that, I learned that after I accidentally killed Dialga instead of catching it in Diamond. I also learned not to use the master ball on something before the main legend, ( i used it on mesprit and soon regreted it )Maybe I'll do the same. I forgot to add something in regards to your question, but you probably already know if you are smart enough. You have to save before you encounter Rayquaza, or any other legendary. Once you do that, then just talk to it and battle it, if it doesn't come out shiny, just reset the game and try again. It's gonna take you some time, days maybe, but don't lose hope, if you really want a shiny that bad just keep at it until you get it.