Or did he ever had it in the first place?
My attention was brought to this via Hamish's blog at Physics World. He pointed out the sharp critique against Nye in Sabine Hossenfelder's "Back Reaction" blog entry. It all stemmed from Nye's video answering a question regarding quantum entanglement, where it appears that Nye got tangled in it himself.
You may read the criticism yourself (be warned, there are some "colorful" language being used in there).
I think that while Nye has done quite a bit in the media to popularize science, I often find his off-script or unscripted responses a bit suspect at times. This is another one such example. It is my impression that he knows the pop-science version of science, but not the intimate detail. Of course, you often do not need the intimate detail when dealing with the general public, which is why he could manage to do this for this long. But when confronted with something that requires a bit more in-depth knowledge, especially in physics, this is where he trips.
I don't know why he doesn't consult an expert when he responded to this person in this video clip. After all, I'm sure it isn't "live", and he could have easily checked if what he was saying was accurate, or nonsensical. Unfortunately, he went into the realm of nonsensical, and he didn't even realize it.