An executive order cannot limit a President. There is no constitutional requirement for a President to issue a new executive order whenever he wishes to depart from the terms of a previous executive order. Rather than violate an executive order, the President has instead modified or waived it.
The President, exercising his constitutional authority under Article II, can determine whether an action is a lawful exercise of the President's authority under Article II.
The Department of Justice is bound by the President's legal determinations. [my emphasis]
Our Constitution has as its most elemental provision the separation of governmental powers into three separate branches. When the government feels it necessary to spy on its own citizens, each branch has a role.