A (French citizen) friend who lives in the US as an H1-B worker recently went on a trip to Croatia from the US. He did not visit any other countries, and both directions of his flight were nonstop between the US and Croatia. While there, he applied for a National Interest Exception from the US Embassy in France, through email, to prepare for a possible future trip to France.
He attempted to return to the US from Dubrovnik, but was not let onto the plane. Probably after a computer warning, the gate attendant called CBP, who confirmed he was not allowed to board the flight.
His H1-B visa stamp is still valid for a few months, his passport for a few years, and he's still employed.
Since he did not enter any Schengen (or other restricted) countries on this trip, I don't think the status of his NIE request should impact his ability to reenter the US. Are there any policies to that effect? Is it possible the airline made a mistake or miscommunicated with CBP?
Apologies for the second hand story, I'm considering doing something similar and am curious if there are any rules I've missed.