In fact, the Egyptians and Syrians had stopped their drive toward Israel, and the counter attacks had already started by October 8. By the time the American airlift began (on October 13), the IDF had already effectively stopped the Eygptian forces from further advance and pushed the Syrian forces past the 1967 ceasefire line and were counter attacking toward Damascus. In other words, a connection between the supposed atomic bombs and the airlift are speculation - not history. Further, one might ask: If Israel did have nuclear weapons and did perceive an real, existential danger, then the prudent move would have been to prepare them in reserve? What's more, if a non-Israeli military plane was flying over Israel during a war, then one would think that Israel would reasonably try to shoot it down. In other words, I don't really know what you're going on about.
World Jewish Congress: Nazi train treasures must go to rightful owners (Reuters)
from the article: Gates: Israel doesn't pose nuclear threat like Iran