I would do it by hand. That way you can go super duper slow and check your progress. If you use really fine paper and go very slow you shouldn't ruin the polish. Also, if the floor guy did it properly there should be more than one coat of poly on the floor. My guess is that you just damaged the top layer because it didn't set quite long enough. So you'll basically just be taking off the top layer with the paper and not even reaching the polish.