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You've probably misunderstood what Xur's upgrades are for. His weapon upgrades are only for exotics obtained [i]before[/i] the dark below was released. They were stuck at a max of 300 atk, but Xur's upgrade gives them the new max of 331 atk. [url=https://www.bungie.net/en/Help/Article/12457][b]Exotic Upgrade FAQ[/b][/url]
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Cause you already upgraded it, the exotic shard, at the end of the process, it wasn't a additional upgrade