Chan-Pomerleano-Ueda proved HMS between the smoothing X and the crepant resolution Y of the (local) conifold singularity. We study the operation on the Fukaya category of X which is expected to be mirror to the flop on Y. On the other hand, there is another mirror construction using special Lagrangian spheres in X and their formal deformation theory, which gives a noncommutative resolution of the conifold. I will explain how this noncommutative mirror behaves when we perform the operation on X, and give an interpretation related to stability conditions. This is a joint work with Y.-W. Fan, S.-C. Lau, and S.-T. Yau.