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Managing Jira Deleted Issues

The Jira Deleted Issues Report is used to view Jira Align work items linked to Jira Software Issues for which Jira Align can no longer access via the API.

Typically there are two conditions that cause items to show up in the Deleted Issues Report:

1) Jira Issues linked to Jira Align items have been permanently deleted by a user in Jira Software.

2) Jira Issues that had their parent project's permissions changed so that the Jira Software Connector Service Account no longer has permissions to view the issue.

The report will display the Jira Software Key, the type of Jira Align work item (as an icon) and its ID, and the work item’s name in Jira Align. 

Note: The Jira Deleted Issue Report transmits a large amount of API Calls between Jira Align and your Jira Software environment. It is highly recommended to run this report once a week, and schedule the run during non-working hours to prevent any interruptions to the regular sync of data.

To manage Jira deleted issues:

  1. Open the Jira Deleted Issues tab.
  2. Select a date and time to run the check. To run the report as soon as possible, enter the current date and next upcoming hour. For example, if it is 3:30PM, schedule the report to run at 4PM. The hour you choose to run the report will be in the Time Zone selected in your personal preferences. 
  3. Click the Check for deleted Issues button.
  4. After the report query has been completed, set Hierarchy and PI Filters in the context menu or locally on the page to parse data. Selections made on the page will override the Configuration bar once the Filter button is selected.
  5. Click the Error Types Field and Filter on Only 'Issue does not exist'
  6. View the report:
    • Click the link under the Jira Key column to view the item in Jira. It may still exist but have a new name.
    • Click the link under the ID column to view the item in Jira Align.
  7. Toggle-on the sliders to the right of each item you want to delete, remove the Jira Software key from, or ignore.
  8. On the toolbar, select one of the following options:
    • Delete. Remove all selected items from Jira Align.
    • Remove Jira Key. Delete the Jira Software keys associated with the selected Jira Align work items. This will keep the Jira Align items and disconnect the Jira Software issue from them.
    • Ignore. Remove all selected Jira Align work items from this report. This will keep the item in Jira Align and leave the Jira Software keys connected to the item. Ignored items may appear again in a future report if the items are still not found in the future.
  9. Alternatively, select one of the Delete All, Ignore All, or Remove Jira Key All options to affect all items returned by the report. Note that these options will delete, ignore, or remove the Jira key from all items found by the report, including those not visible on the current page of results.

Note:   Issues displayed with a red warning indicate that the Jira Parent Project Permissions changed or the issue was deleted in Jira Software. The report also displays API parsing errors via a yellow icon; the parsing errors should be ignored or filtered out using the Error Types, as the issues still exist in Jira Software.

Note:  In current versions of Jira Align, the report no longer searches for accepted stories and features, as well as closed defects. 


Shawn Kessler
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
Feb 07, 2020

Great write up @Kent Baxley ! Much needed in the Community!

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Great Article! Thanks for the guidance! Perhaps including that the Jira Deleted Issues tab can be found under Administration → Connectors → Jira Management would be helpful as well! Just a suggestion.

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Derek Huether
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
Mar 02, 2022

2 years later, this is still a super valuable article! 

We Try to delete a Program created for testing (ZZZ DELETE ME) But had a lot of associates Issues. we get rid of all of them, but forgot One Story (3 TEST A) from that program, related to a Project ALIGN PROD TEST that does not exist anymore as had been deleted, and the project as well.

Now the Story still shows in Teams and Program can't be deleted cause of this orphan Story.

We ran the deleted Issues execution on Jira Align but doesn't bring nothing at all (Probably because it looks first at the Projects declared on Jira Align, and this is not anymore)

Any Ideas in how to get rid of it ?

Colin Weaver
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
Jun 29, 2022

For info of others, (as I believe Andres already knows) you can delete a story in Jira Align, by opening the details of that story and then using the More Options link found in the right side bar.

The Deleted Issues report will show stories deleted from Jira as long as the Jira Project and Board configuration still exists in Jira Settings / Jira Management. However if the configuration has been removed then then the report may show no information and will mean to clean up the orphans will require individual removal of stories, features etc, using the choices  available under More Options 

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