Yes, they will. The general advice is to not expect your items at resort #2 until late in the day, like 5pm to be safe (although it should be a little earlier… but can be later!). Make sure to pack a day bag with anything critical you may need during the changeover (medication, bathing suits, change of clothes, dinner attire if you have an early dinner you might not make if your bags are running late, etc). If you are at all worried about the logistics/planning implications of late arriving luggage most will recommend to rideshare or taxi to resort #2 that AM with your bags and drop off at bell services (assuming your room is not ready) - that way you at least know where you luggage is and can physically access it at all times in case something goes screwy. But if none of that is a concern and you want to hit the parks ASAP that morning, having Disney move your bags is a great option.
Enjoy your stay!