When you say someone has nodded in agreement it is meant that they are lowering and raising their head to signify their agreeance without needing to say anything.
There is a more subtle version of this, quite common in film, where Character A is asked a question and Character B responds by essentially blinking in agreement or by nodding with their eyes/eyelids. They do not move their head, and they may say something, but usually when they don't it used to deliberately not make it 100% clear to the audience what Character B's intentions are. I can't think of a specific example but I have seen it especially in high tension situations when a group of characters are trying to determine what side of the fence each person is, or during interrogation scenes.
Example 1 (bold part is what needs replacing):
After the meeting, Paul walks straight up to John, deliberately menacing.
"So I hear that you're going to fire Tom?" demands Paul.
John nods with his eyes, wary of the attention from the other colleagues in the room.
"Was that a yes then?"
John nods with his eyes again, "We should talk about this privately, Paul. So we don't disturb the other workers."
"You really are a coward John!"
Example 2 (bold part is what needs replacing):
"Paul, were you or were you not at the suspects house 2 nights ago?" asks Officer John.
Paul nods with his eyes.
"Was that a yes? Please verbally confirm for the audio recording."
Paul again nods with his eyes, answering John but not letting his answer be recorded.
"Dammit, you answer me Paul!"
Best Answer
I think you'll find that in most cases, a person would find "blinking in agreement or by nodding with their eyes/eyelids" quite hard to interpret as a definite yes or no. It's not surprising, therefore, that we don't have a single word for it.
However, your description of "nodding with their eyes/eyelids" sounds like a wink. A wink can certainly be used to indicate "you're in on my secret", and would commonly be accompanied by the subtlest of nods as indication of unspoken agreement.
As might be obvious from some of the above examples, a wink is ambiguous in the absence of the tiny nod or other signal to confirm intent. It might instead mean (or be interpreted as) "don't believe me, I'm being duplicitous", or even "beware, it's dangerous". In other words, a wink might not indicate agreement, or conversely it might indeed indicate agreement but might not be interpreted that way. Context, knowledge of the other person and body language are everything here!