I do not think that the protection exists "at the highest levels" - after all, those same "highest levels" created the Snake Eater teams to investigate and potentially destroy the Project post-war, and it is ridiculous that their existence was not matched by a significant pre-war investigative effort as well. The Project no doubt had some allies in a few key positions, but it could not be more than a tiny, tiny fraction of the government.
The fact that the Project already required the active participation of big movers in science and industry means that they had tremendous resources as well as a time-travelling patron. Indeed, a packet of files pressed into the hands of BEM at the right time would give the Project plenty of warning to sidestep anything that would significantly expose the Project.
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