Energy and entropy are not really the right metric here. The thing that is lost when a species goes extinct is information, and specifically, information that has been acquired by a process of parallel search that has been going on for literally a few billion years, so the odds of reproducing that information once it is lost is effectively zero. Imagine working on a term paper for a few billion years and then having your computer crash and not having a backup. That's what happens when a species goes extinct.