That's how the exotic "upgrade" system works. If you trade-in an exotic (even a v2 exotic), all XP progress is reset.
If you have a v2 exotic armor piece, the only reason to trade it in would be if you like the stat roll of the one Xur has better. The UI will let you trade in a v2 exotic for a v2 exotic.
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Exotics have set perks. You can't reroll those.
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Edited by YapperFlapper: 1/16/2015 5:43:13 PMThat's why I said "stat roll", not perks. Strength, intellect, and discipline rolls can vary on exotics. Xur is selling a hunter helmet with higher discipline than the one he has for "upgrade" this week.
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Ah right, gotcha