Hello, Eamon! If you have a valid maintenance license, I suggest you raise a support request with us at: https://support.atlassian.com/contact/
I believe this might require assistance verifying the data inconsistency that seems to be causing the issue. Otherwise, give it a look at this and see if it fits your scenario: https://confluence.atlassian.com/jirakb/how-to-fix-the-duplicate-agile-custom-fields-after-upgrading-779159142.html
If the kb does not fit your scenario or the procedure does not help, please share some more information like the versions (from and to) sharing some logs of what happens when you try to do something with the fields, as well as an image to give us some context.
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