This paper presents an enhancement for use in advanced trajectory management automation systems for addressing issues associated with aircraft not conforming to their route and altitude assignments. It also addresses integration issues when tactical and strategic conflict resolution services are provided by different sources. The enhancement is being added to an automation concept referred to as the Advanced Airspace Concept (AAC) that is being developed to meet the needs of the air transportation system beyond NextGen. A flight plan route and assigned altitude conformance monitor is added to the AAC. In addition, a mechanism to define out-of-conformance tolerance thresholds, and a solution, referred to as Recapture, to resolve out-of-conformance flights is proposed. Furthermore, this paper introduces a trajectory refinement concept for rejoining an aircraft with its route or assigned altitude especially following an open-ended separation maneuver such as a single heading vector or temporary altitude. These new capabilities enable the integration of the Autoresolver and Tactical Separation-Assured Flight Environment, or any other separation agent, so the transition of strategic and tactical separation assurance responsibility is seamless. A set of fast-time simulations are performed to support the proof of concept, and a survey of operational applications are explored.