You can delete queues from a connection profile using the delete feature.
Deleting a queue definition does not affect the referenced end-point because an endpoint is self-contained. If a queue exists at runtime, its deployed service package works as designed.
To delete a queue from a connection profile:
Expand the Message Transports category and navigate to the JMS provider from which you want to delete a queue.
Right-click the queue and select Delete Queue Definition from the context menu.
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