Hi Mark,
I have imported your POSCAR_before into VNL, and then exported the corresponding structure to POSCAR. VNL does export it in the original format. So, this is a plugin version issue indeed. I assume that you did not manually change the lattice type from 'Unit Cell' to 'Hexagonal' in 'Lattice Parameters' after importing POSCAR_before. This is when VNL would convert it in accordance with its internal convention for a hexagonal lattice.
For your information, VASP should work without any problem for the hexagonal lattice vectors as defined in POSCAR_after, at least according to my experience. In fact, this definition is considered as conventional for hexagonal lattices, see Setyawan&Curtarolo, Computational Materials Science 49 (2010) 299–312.
Regards,
Petr