Board Thread:Lore Discussion/@comment-71.61.178.23-20130623221624/@comment-9887604-20130625044852

It's also possible that the Limothiit were wiped out much earlier, during the first era the Thrassian Plague ravaged Tamriel.

"Traveling down the trade routes into the heart of Elsweyr, the plague decimated the Khajiit, forcing the survivors into roles they did not choose. Thus was the province turned from sixteen states to only two: Pa'alatiin and Ne Quin-al, more commonly known by their Cyrodilic names of Pellitine and Anequina." Pocket guide to the Empire 3rd edition

The Limothiit may have been one of the 16 kingdoms that was wiped out by the plague. It's also important to remember that Khajiit vary wildly in their appearance, depending on the phasing of the moons during their birth. It is possible that some slight change in the orbit of the moons may have changed the chance of certain kinds of Khajiit being born.