The only one I can think of is it'll mess up the Unity Tower data for some of the trainers you "traded" with, but only if they don't have GTS metadata (ie, if they don't have a custom trainer sprite on Pokécheck), but that doesn't matter. Just make sure your change your DNS back to auto-obtain if you're going to compete in official events like VGCs.

Hi! Sorry to bug you, but I kinda wanted to use your Pokemon for the 2013 International Friendly. Just wondering if there's any negative side effects associated with downloading .pkm files or using Pokemon obtained from .pkm files in official events?
Thanks~!