Military weapon systems are a war unto themselves: each side learning about the other's and creating new systems to remove those advantages. Basically, once the F117A became common knowledge, it was only a matter of years before modern radar systems were developed that mitigated that advantage.

I have little doubt that Russia put a lot of effort into making the S400 effective against stealth aircraft. Having a low radar profile still helps, but we won't see the advantage the F117A had over Baghdad.