It is normal for an E-4B to accompany the President, Secretary of Defense, and the JCS if they travel away from DC or one of the major bases in the US.
They may travel on AF1 or another plane or on the E-4B depends on the situation.
>To provide direct support to the President, the Secretary of Defense, and the JCS, at least one E-4B NAOC is always on 24-hour alert, 7-days a week, with a global watch team at one of many selected bases throughout the world.
https://www.af.mil/About-Us/Fact-Sheets/Display/Article/104503/e-4b/