Countless times this has happened.....Okay, just three times. In Blue *eye twitches* after getting 150 Pokemon. In Crystal (which wasn't too bad, since I barely played it since I was pretty much done with Johto after playing Gold for hours), and in Sapphire, after JUST beating Wattson, the hardest Gym Leader I ever fought (I hated how there were no fire types available until far into the game), my brother saved over my file AGAIN.
Now, I NEVER let him touch my games, since he has his own and more. >>
My brother's systems? He has his own PS3, DS 'phat', a DSi, a PSP, and a N64 (jerk!)
My systems? A single, humble DS lite.
And we all share the Wii, which my parents mostly use.