If the White House declares something secret then they have acknowledged that it is true.

This makes declaring parts of Bolton's book secret a bit more complicated. So Trump has several choices to try and cover this as he admits it true by declaring it a secret. It is hard to guess what the main one is going to finally solidify as, but we have several examples of what Trump will try to do:
1 Declare that he does not know John Bolton.
2 Declare that John Bolton was just a coffee boy.
3 Declare that John Bolton has very poor ratings, and no one watches his show.
4 Declare that John Bolton is a liar, and no one likes him.
5 Declare that he doesn't like John Bolton because he prefers people who didn't get captured by the enemy.
6 Ask who will rid me of this turbulent priest.
7 Have John Barron call a reporter to tell them that Bolton is impotent.
8 Threaten to sue John Bolton for libel. Quickly drop this quietly but sort of continue threatening.
9 Go on a full-blown regular twitter rant projecting all of his own sins on Bolton.

The only silver lining in this is that no matter what happens it causes Trump and Bolton grief. For me that is win-win.