I think you are spot on - you can't apply it retroactively in this case. If you set it up as H(H(pwd, salt), pepper), you could apply pepper retroactively, but

I think you are spot on - you can't apply it retroactively in this case. If you set it up as H(H(pwd, salt), pepper), you could apply pepper retroactively, but that's not what's proposed here nor in the SO question linked above. Also if you do H(H(pwd, salt), pepper), you can successively apply new peppers and make it a bit more maintainable, but I am unclear that it is secure to do so.