You dont have to take the cards out of the system to check the "bad" card..
Specify the cards in your bat file. -di 0,1,2,3,4...... Go to steps... -di 0, check if it working.. Instert -di 1.. check if its working... And so on.. It will save you some time with rebootig and taking your cards out

Sorry, how exactly would I do that in the bat file? Just -di GPU0 to disconnect that card?