We recognize that due to the connector between Jira and Align, that permanent delete creates a challenge, however, due to configuration and restrictions, it adds a tremendous amount of manual overhead to do things like "move a feature to a new program":
1) Delete the ones attached to the wrong program in Align
2) Delete the ones in the wrong project in Jira
3) Empty the recycle bin
4) Reimport (features) into Align

We use the API and automation to perform actions such as this from other systems, and cannot due to the lock placed on the Jira Project field.