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WDM optical networks represent the direction to the future high capacity wide-area network applications. By reconfiguring the logical topology, network resources utilization can be optimized corresponding to the traffic pattern changes. From the viewpoint of network operation, the complexity of reconfiguration should be minimized as well. We consider the logical topology reconfiguration in arbitrary topology IP over WDM networks with balance between network performance and operation complexity. The exact formulation of the logical topology reconfiguration problem is usually given as a mixed integer linear programming, but it grows intractable with increasing size of network. Here we propose a simulated annealing approach to determine the target topology with a smaller logical topology change and satisfy the performance requirement. A threshold on the congestion performance requirement is used to balance the optimal congestion requirement and operation complexity by tuning this threshold to a feasible value. For an effective solution discovery, a two-stage SA algorithm is developed for multiple objectives optimization.