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There is a retroactive fix planned, and I’ve also been told that we’ll be using a GW1-style token system so you can choose a better reward item when you complete the story. (We agree that three green items isn’t cool enough.) I wouldn’t expect to see the new rewards and retro fix until the 10/28 update, though, because the upcoming holiday content is eating up our precious testing time.
As far as I know, any character who has completed the story will receive mail with the new reward(s). We’re not transmuting the old rewards or searching the character’s inventory for them, etc. so it doesn’t matter if you sold/salvaged/deleted them.