John,
I assume you have informed the custy that the filtration marks may not fully come out. Having done that, personally, what I would do is - prespray with M/S, pure clean or other and then rinse with Ultimate Master or Hydra Dri. This will bring up as good a result as any, and will be okay to apply protector afterwards, although I dont think they work as well on cleaned carpets as they do on new, no matter how neutral you leave the carpet.
Dave.