Connecting flight and checked luggage with Iberia

Next week I will fly by plane for the first time.

I have checked baggage in my itinerary and it says it applies to PRG – SDR. However, there is a transfer in madrid. The itinerary says I should arrive at terminal T4 (not T4S). Is that possible? I have to wait more than 12 hours in Madrid. Both flights are from Iberia, and the company says on its website that I have to check my luggage again in this case.

Does this mean that I have to pick up my baggage at Terminal 4 and walk completely out of the terminal and do the whole procedure again? Will my boarding pass still work?

Edit.
http://help.iberia.com/frequently_asked_question/luggage-check-in-on-flights-with-stopovers-or-connections/
(see exceptions)

Departure time into Madrid is 18.50 (31.8). Next departure at 7.40 (1.9.).