The gene pool of a species is much more dynamic than you assume in your scenario. Combinations, deletions, mutations, introduction of new genes from other speci

The gene pool of a species is much more dynamic than you assume in your scenario. Combinations, deletions, mutations, introduction of new genes from other species is very common on biological timelines. To put it as an optimization problem: a huge portion of the search space has been (and is actively being) searched already, with the current species as the optimal solution for the given ecological niche. Changing the genomic setup will with a high likelihood move away from this optimum, rendering your "new" species less fit for its niche.