Here's the KB article that Mathias mentioned: https://confluence.atlassian.com/display/GHKB/How+to+Fix+the+Duplicate+GreenHopper+Custom+Fields+After+Upgrading
Do be careful with the steps and check if any data has been entered for the duplicate fields. Perform a full backup of your data and home directory before perform such modification. If you have any doubts or issue, please raise a support to Atlassian as Engineer can advise and help you to look into the problem as well.
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