So I went to route 9 with everything going smooth and then I found the hidden grotto. I interacted with and fought one of the honedge that can be found there. In the battle I had a stupid moment and killed it with my delta gardevoir using nuzzle. After it ended, I thought no sweat I can just go out then back in. After doing so, the honedge is there but I can’t interact with it to start the battle. I have tried going in and back out multiple times.
Edit:After searching the grotto in route 8 to see if this problem applies to all overworld wild pokemon (It still worked), I returned to the grotto in route 9 to find that the pokemon are no longer showing up period.
Most grotto pokemon respawn after a full 24 IRL hours if not mistaken. So try again in a day or two. If you still cannot interact, then I’m not sure.