You cannot remove an entry form vault with the vault tool. You can choose only amog following options "0: Store a password 1: Check whether password exists 2: Exit" Pleas add "remove password" option to vault tool (vault.sh)
Functionality verified in EAP 6.4.0.DR10
https://github.com/jbossas/jboss-eap/pull/2073 for test
John Doyle <jdoyle> updated the status of jira EAP6-249 to Closed