If the Khajiit are a stone and the moons are a tower, then isn't it possible that a civil war between the Khajiit or the death of the Mane (I believe he died during this time) caused the moons to dissapear? And only when peace was made again and a new mane was installed did peace return and with that the moons?
That's my theory at least, why in heavens name they would thank the Altmer for returning the moons then is beyond me, but still.
The Mane was assassinated before Infernal City, so you've got about 30-40 years between death of the Mane, the splitting into city-states, and this alleged civil war. Granted, when not unified by a singular ruler, the chance of warring of any kind is greater, especially since Anequina and Pellitine have had history of conflicts in the past. But then again, on the other other hand, Khajiit have warred in the past and the moons have not gone away...
Edit: I need to read the whole topic before dredging up old points.