From what I understand cooper later recanted some elements in it, claiming the information he was fed was false/disinformation, so it's hard to say

The Krill documents that were given to him by John Lear was what he realized was disinfo. You're right that at one time he did believe aliens but towards the end realized it was discrediting tactic. That's not to say the UFO he saw was disinfo, he ended believing that all the aliens documents he saw were meant as a cover story for new propulsion systems that had been developed in the Skunkworks.