In Our Man Flint, Z.O.W.I.E. appears to be a multi-national organization, reporting to a collection of representatives comparable to the United Nations Security Council. In this guise, individual secret agents are dispatched to handle particular cases. Agent 0008 and Derek Flint are notable agents. Though the work itself appears to be covert while in progress, the agents gain a certain amount of notoriety. In particular, Agent 0008 found himself the subject of a series of action novels.
This is in stark contrast to the depiction of Z.O.W.I.E. in In Like Flint. In this film, Z.O.W.I.E. head Lloyd Cramden reports directly to the President of the United States, who relieves him of duty. In addition, the organization has a military hierarchy of officers, recruits through advertising campaigns, and presides over certain large-scale operations, such as an orbital space platform.
While these are not mutually-exclusive depictions, they form one of several significant points of discontinuity.