From the military viewpoint though this would take resources away from the fighting fronts to conduct extra anti-partisan patrols. Other military governors of occupied lands would take note and step up their security measures at the expense of any working relations with the locals. Reinforce the viewpoint among the German soldiers that they can't trust any Czechs creating a 'siege' mentality that separates them from the populace and makes them even more heavy handed in day to day life (aside from the actual reprisals). The Czech resistance would probably find more recruits and help in the long run as the reprisals spread the fear and hatred of the German occupation and spur more fence sitters into action against the Germans.
Perhaps no outcome on the length of the war in the big picture but having Bohemia and Moravia with their arms industries hosting any sort of resistance be it in outward fighting or sabotage of the production works all adds to the final victory over the Germans. Keep in mind that 'Total War' doesn't just blur but usually erases the care toward civilians in that they are too the means of production for the enemies war effort.
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