It makes no sense since that doesn't exist in any Pokemon game I've ever played. I assumed they'd be tracked on the trainer card like in the Pokemon games. Since there doesn't seem to be a command to give a badge, I figure my best bet is to just beat him again.
However it doesn't let me, so I need to reset whatever is telling the game I defeated him already. My best guess was the gyminfo.dat, but it's not in there. It did tell me that it was supposed to be the zephyr badge though. I'm using NBTExplorer to read the .dat files.
Edit:
I was using 7.2.2, but just updated to 7.3.1.