No because of the way genetics works it is much more likely to be the Y chromosome that is lost. First the Y chromosome is under stronger indirect selection tha

No because of the way genetics works it is much more likely to be the Y chromosome that is lost. First the Y chromosome is under stronger indirect selection than the mitochondria due to asymmetric mating. Second in mammals when two different species have a genetic incompatibility this incompatibility manifests in the male offspring. Both of theses point towards male Neanderthal female African as the way this hybridization happened. Edit. I should add the scientific paper behind this New Scientist article proposes a precise genetic mechanism for how the Neanderthal Y chromosome is lost which is further evidence the loss is due Y Chromosome incompatibility.