I would think the Emperor should get a relations penalty with the country, if they still exist, that gave up the land as that nation agreed to give it up. The Emperor shouldn't get to request the province(s) back regardless as they lost the war, even if they weren't the war leader (I've lost provinces when I wasn't the war leader, I didn't get to request them back, I got the reconquest CB instead, I had to wait for the truce to finish).
One of the main premises of the HRE is to defend small nation states from larger forces outside the HRE, if the Emperor is derelict in that duty, that's the Emperor's problem, not the attacker's, to the point that every member of the HRE should get a relations hit with the Emperor for allowing a province to fall under control of a non-member on top of the IA hit that goes along with that.