I don't see why it would change anything. But in any case I've heard to drink the ACV with water and then either put a bit of baking soda in your mouth, or dilute the baking soda in a bit of water and swich it around.
Personally, I use a straw and stick the end way back in my mouth. I know some gets on my teeth, but I always wait about a half an hour and then brush. Don't brush right after!