I admit its entirely circumstantial (as you would expect the evidence to be for something that would be so secret). Other than anecdotes, there were many publicly acknowledged anti-gravity research programs in the 50s and 60s that ended up being classified with no further information available, there is testimony hinting at some kind of revolutionary propulsion technology like the black project scientist's claims I mentioned earlier, as well as two claims of Ben Rich, former head of Skunkworks: The first, that they made multiple breakthroughs in propulsion over the decades he was there that are still top secret; the second, that some UFO sightings, with all their incredible aerodynamic properties, are sightings of classified craft.
During the Nimitz tictac encounter, the pilots involved mentioned apparent civilians who came in and took the data collected from instruments. It's open tot interpretation what the deal is with that, but I think it's far more likely that it was because they wanted data on an encounter between a classified drone operating on revolutionary propulsion and conventional aircraft.
There's nothing definitive when it comes to this subject, but its all worth considering.