Why did Robert Kennedy respond to Khrushchev's first letter but ignore the second letter?

Simply put, the first letter from Khrushchev was more conciliatory, giving JFK a glimmer of hope that the missiles would be removed from Cuba without escalation. The second letter that came was more aggressive in nature, stating the Soviet Union would retaliate if provoked. Also, the first was a private letter believed to be from a stressed Khrushchev personally, whereas the second was a public statement believed to be dictated by the hardliners in the Soviet government.
By answering the first and ignoring the second, JFK was able to set the parameters of the ongoing debate over the Soviet missiles in Cuba, ultimately leading to the removal of the missiles without further incident.