Ahh, game file horror stories...
I had about 90 Pokemon in my first Red version, and six badges (around 40-50 hours, not to mention the trading). I went out to play outside with one of my cousins, and let the other cousin start a new game ('without saving' she says.) When I go turn it on again, I had one badge, a Bulbasaur, Rattata and Pidgey.
/cry