[0] https://skyriddles.wordpress.com/2018/01/21/nasas-long-dead-...
The instances you're thinking of are either "lost" as in "presumed dead" (like IMAGE) or non-Earth orbit probes (like ISEE-3). IMAGE was never untracked, and ISEE-3 was never supposed to be tracked (but its location was still known.)
Remember when the NRO gave NASA two space telescopes no one knew they even had, bother where comparable in scope/complexity to Hubble.
The only reference I can find for this says the NRO satellites won't be launch till 2020. They're not up in orbit.
[0] https://www.space.com/16000-spy-satellites-space-telescopes-...
If they are handing over that kind of technology I wouldn’t rule out them having some amazing tracking stuff we know nothing about and won’t for a decade or two if ever.