If whifnium did exist, but it was completely unobtainable, then both physicists would still not be able to extract any work out of the system. If the one that didn't know about whifnium was given some amount of it without being told what it was, and instructed in how to use it, they would still see the same amount of work being done with it as the one who did know. They would just find out that they were wrong in their calculation of the entropy of the system, even if they still didn't know how or why.
And of course, this also proves that the system had the same entropy even before humanity existed, and so the knowledge of the existence of whifnium is irrelevant to the entropy of the system. It of course affects our measurement of that entropy, and it affects the amount of work we can get that system to perform, but it changes nothing about the system itself and its entropy (unless of course you tautologically define entropy as the amount of work the experimenter/humanity can extract from the system).