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Starting in JBoss EAP 6.4, you can delete existing entries with the interactive vault tool. To be specific, there is an option "Remove secured attribute".
I just validated it with 6.4 and I am able to see the remove option. Unfortunately our stack is on 6.3.0 EAP , therefore we will have to find out another way.
I'm wondering if you can use the 6.4 bits to manage your vault, and retain the 6.3 bits for production until you're ready to upgrade?