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Well as far as I remember, Scotty says he beamed the favorite beagle of the president. They don't mention porthos by name.
It is probable that Archer is alive due to advances in medicine in the future. It is probable that when Porthos eventually died he got a new dog :) , or again with the appropriate pills Porthos became the oldest beagle on the planet(before Scotty beamed him into oblivion :D )