I recently had a Wifi Battle, I didnt save the game cause I didn't think much about the battle. Anyhow both of my Pokemon in a doubles battle lost their items permanently. I think the opponent use a move thief, but I know she took both of my Pokemon items in the battle. When I log off from the battle online, I see both items have disappeared. What just occurred? and both items cost me 48 Battle points each. Basically this person made me loose 3 hours at the battle tree. Help!!!
Items that get stolen/used online get returned after the battle. And like SYL (SeeYaLater!) said, the game saves before you battle (It happens while you're connecting to the internet, the game doesn't save after the battle). The game only doesn't save when you're entering quick link battles. I doubt Game Freak would make such a ridiculous feature where you can keep stolen items from online, that's not fair for the opponent you stole from. I stole an item from my brother's Zekrom with Hoopa's ability. My brother didn't complain that his item was gone after the battle, because it wasn't. It was probably just a glitch or there's something with your cartridge/3DS.
I hope I helped.