The original Desmond probably died in the explosion at the end of sesaon #2.
If you recall Desmond says his life flashed before his eyes, as many people say when comfronting "Death". Also what do all creatures, human and non human have in common. You guessed it, we are all born naked. Desmond wakes up on the island after the explosion, you guessed it, naked. He was probably reborn, but is not the same Desmond as we know. That is why the reflection of him in the jewlery store appears older and or alien.
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