Oh yeah, if you run from a Trainer Battle, it acts like all your Pokémon fainted and you get teleported to the Pokémon Center. I should know since I accidentally fought the endgame trainer outside of the Pokémon League when I had just started the Treasure Hunt, there was no way to win so I had to run. Sorry for your loss.

I feel the pain. I've encountered about 17 shinys, caught 2. I died inside when I lost the shiny Norveirn.