You just need to give the two fix reax/c/species commands different file names for species.out and pos output files, because the second instance overwrites the output files from the first instance. E.g.
fix 7 all reax/c/species 1 1 25000 species_npt.out position 25000 molecules_mass_center_npt.pos.*
fix 7 all reax/c/species 1 1 25000 species_nvt.out position 25000 molecules_mass_center_nvt.pos.*