The integrated automatic shipment handling systems (IASHSs) in large freight terminals and distribution centers are complex and increasingly congested due to the increase of freight volume. Shipments in IASHS need to be handled by a large amount of equipment. Thus, optimization-based tactical and operational planning models and methods for how the shipments are routed through the network of equipment in IASHS are required. To reduce the total shipment travel time, this paper studies a flow diversion strategy for routing shipments from their origins to their destinations, using multiple paths. This strategy is further leveraged to develop a destination reassignment strategy and time control strategy. We formulate these strategies as mathematical models and evaluate their effectiveness in static and adaptive implementations via numerical experiments. They are also compared to the classical shortest path oriented strategies.