The F-117A stealth fighter flew for several years before being revealed to the public but it's a relatively small and quite airplane that flew most of its flights at night. Lyndon Johnson unveiled the Blackbird in 1964 (I think it was the Air Force inteceptor YF-12A version) when the plane's test flights couldn't be confined to Groom Lake with a reasonable expectation of privacy. A very fast aircraft needs a lot of room to maneuver, so confining it to a small area is very difficult. The Air Force unveiled the B-2 before its first flight because they needed to do the early flights in the daytime (and the first flight was from the factory in Palmdale to Edwards AFB) and you couldn't very well keep that secret. The "Aviation Leak & Space Trechery" article mentioned that someone saw the plane in the middle of the afternoon over Utah - something that seems unlikely for a "black" program.

I'm not saying that the article is false - it just seems somewhat implausible to me. A coworker who was an SR-71 RSO says it's plausible to him (perhaps he knows and can't tell or is just speculating). Such a plane could be powered by several of the SR-71's engines. That would save a lot of development time & money. The article mentioned that they used leftover Valkyrie materials (the plane was built largely out of stainless steel) to build the Mach 3.3 mothership.

Did it happen? I don't know - but I'd like to.