Before Day 5 Edit
CTU used the protocol "flank 2" as a code word, meaning that the agent using the terminology was operating under duress; and therefore, was being manipulated by the hostage-takers to feed false information to their home agency. When agents reported to be under duress, CTU automatically red-flagged these situations within their transcripts.
The protocol for duress changed to another term sometime before Jack Bauer's resurgence.
Day 5 Edit
During Day 5, Jack Bauer was secluded from terrorists that had taken control of Ontario Airport. He used this opportunity to provide reconnaissance to CTU. Without CTU's knowledge, Jack was ultimately captured by the terrorists. The terrorists took advantage of the fact that Jack was providing information to CTU, and coerced him to tell them information that would give the terrorists the upper hand. When giving the information to Curtis Manning, Jack added that he was in a "flank 2 position," but CTU failed to recognize Jack's word usage at first.
CTU field agents were about to strike the terrorists, using Jack's faulty reconnaissance, when, at the last minute, Lynn McGill halted the operation after making the connection that Jack Bauer had no knowledge of the protocol updates; and therefore, did not know that "flank two" no longer meant "duress."