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Start with a normal neutral-evil human character. He gains the half-fiend template and is now a NE outsider (native). Later, he is transformed into an undead with the augmented subtype such as a vampire or mummy, presumably leading to a type of undead (augmented outsider, native).
How does the Holy Smite spell affect this character? Does he take 10d6 from it as an evil outsider? Or 5d8 as an evil character irrespective of anything else?
How does a Bane (outsiders (native)) weapon affect him? Or a ranger with favored enemy of the same flavor?
It treats the creatures as if they were "all of the above" - so they take 10d6, and and are subject to Bane as if it were targeting their specific type.
The only reason to retain those elements is to continue to interact with such effects as if it were still those elements. Otherwise, those elements would disappear - that is, be erased and replaced by the new subtype - in fact, that is what used to occur with such things, making the change intentional.
Hope that helps!