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It could be worse. You could encounter a shiny when you don't have pokeballs yet. Then, you would have to KO your first random shiny, or run away from it.
And then, a couple of years later, exactly the same thing could happen on another playthrough, on exactly the same route, with exactly the same pokemon. Yeah, it would really suck if that happened. Especially if that person never found any more shinies after that.
...yep, that really would suck.