You are able to submit a request for the duplicate to be refunded. You may do so as of right now per this dev post. You should get the (600) gems refunded for the duplicate without a problem.
If you are not sure how to submit a ticket, at the top of this page click on “Support”, then in the top right of that page click the “Submit a request” link and fill in all applicable areas.
Purchase Issue
Email address to be contacted at by Support
Subject (Mine will be “Wardrobe – Refund on Duplicate gem store skins”)
Description of the issue
Issue – [No Selection] box – Select “Refund” in the drop-down and then “Gem Purchase”
Your name
Email associated with your account
skip billing section since you used gold > gem conversion
DOB
GW2 Serial
GW2 Name (your ForumName.1234 name)
Submit
Easy peasy.
You should also receive a type of “we’ve received your support request” email, but if you do not receive one of those, please check your spam box. If it’s not there, see this sticky thread also.
Then give them plenty of time to see to your request…there will be many thousands so please be patient while they get to them all.
This is basically my exact situation too, so it saves me a lot of work. XD