I would assume that the two Ditto won't transform, and thus can only use Struggle. But what I also want to know is what would happen if you switched to another Pokémon, then back to Ditto, while facing the same Ditto?
Also, does Struggle do recoil damage like in the normal games?
Best Answer
From this GamePress article:
Also from this page, the video linked in the article directly under "Battling with Ditto" shows that there is no recoil damage for using the move Struggle, contrary to the main series mechanics.
As for having a Ditto transform into a transformed Ditto, according to this compilation of Ditto mechanics:
Additionally, from this article, it appears that attempting to switch a Ditto back in to battle results in your Ditto fainting: