Modern many-core CMPs and MPSoC embedded systems integrate different cores. A 2D mesh interconnects the routers at each core providing system reconfigurability which for instance allows the bypassing of specific routes due to faults or congestion. In this work, a class-based many-core architecture with reconfigurable classes and a 2D Mesh-based on-chip interconnection network is considered. We present an affinity- and distanceaware thread scheduling scheme and migration policies for a reconfigurable heterogeneous class-based 2D Meshinterconnected many-core CMP. We also present a simulator for evaluating various scheduling and migration algorithms. The simulation results reveal that scheduling algorithms which both consider core affinity and support distance-based migration outperform the other considered algorithms in reconfigurable many-core architectures.