mislabeling of periodic boundary conditions with changing geometry

Hi

Problem:

I have a unit cell of a periodic lattice structure. The unit cell has Floquet periodic boundary conditions [PBC], and I am doing a parametric sweep of the geometry features of the basis (the unit cell area doesn't change). The problem is that when the geometry changes become large enough, for example when a feature cross the unit cell boundary on the left it would then appear on the right to preserve the symmetry. But this obviously changes the numbering of the PBCs, and it is not practical to manually select those boundaries for each step in the geometry sweep. Anyone encountered such a problem?

thanks,
Chris