Adding .resize blocks inside setGenericBC() to clear the pbc vectors, which are affected by the mesh treatment operations. This step was to eliminate errors concerning the pbc vector setting coming from the call of contractEdgeByLength(). Such method changes surfMesh.IEN as well as invokes restoreMappingArrays() to build the new element connections. However, there is a specific function that causes the convergence break in the PBC implementation.
Update.