This is an interesting Newsweek piece by Kurt Eichenwald that goes into detail about the NSA's wiretapping program as it relates to the phone call between Michael Flynn, President Donald Trump's former national security advisor and Russian Ambassador Sergey Kislyak.
Assuming the Flynn recording involved RAGTIME-B, because of his position as a former director of the Defense Intelligence Agency and being the incoming president's national security advisor, the intercepted material would be immediately analyzed. If Flynn—as the White House first stated when the news of his contacts with Kislyak became public—had been engaged in pleasantries or planning meeting times for the Russians with Trump, the records of Flynn's side of the conversation would no longer exist. Flynn would have been deemed an American person, and the intercepted recordings and transcripts would be "minimized"—the word used in the surveillance world for when portions or all of an intercepted communication is destroyed. In other words, if the conversation was no more than "How are you Ambassador Kislyak," or "Let's set up a meeting for you and a Russian delegation with the president-elect," Flynn's words would no longer exist in any American file.
But that's not what happened. Instead, something in the recording led the first-level analysts from RAGTIME to follow the next leg of the procedure and take the intercept to the head of the FBI's National Security Division for another review. Again, if a conclusion was reached that there was nothing in the call to raise concerns, the reviews would have stopped there and the data would have been minimized. But the division head instead decided that the intercepted conversation merited bringing the raw transcript to James Comey, the director of the FBI, and his deputy. (At the time, this would have been Mark F. Giuliano, a veteran of the bureau. Giuliano has since retired and, as of this month, was replaced by Andrew G. McCabe, a former lawyer in private practice who joined the federal law enforcement agency in 1996.) The director and his deputy were then the final arbiters of whether the intercepted communications merited further investigation. And they decided it did.