Issue Summary

Once the JS Story is marked as "Deleted" state on JS, JA will delete it and the child JA Task. If later on, the JS Story is changed to a different status on JS, JA will create a new JA Story and child JA Task (both with new Ids), that both points to the original JS Story and JS Task . Now JA will push an update to the JS Story remotelink, so on JS, it reflects back the correct JA work item, but for the JA child Task, the remoteLink is only updated in the situation that a manual update is made on it on JA, otherwise, the JS child subTask remotelink will continue to point to the old JA Task.

Terms in use:
JA Story mapping to JS Story
JA Task mapping to JS Sub-Task

Steps to Reproduce

1. Create a Story on JS
2. Create a Subtask on it
3. Wait for both to sync to JA
4. Now change the JS Story to the mapped Status of Deleted
5. Wait for it to be deleted from JA
6. Change the Story back to a different Status on JS
7. Check JA Task

Expected Results

remotelink on JS Sub-Task would be linked to the correct and current JA Task if JA Tasks still exists.
If JA Task no longer exists, then remotelink would be removed.

Actual Results

JS Sub-Task links to an existing and incorrect JA Task.

Workaround

Not a workaround, but a way to repair:

To fix the remaining links, we would like you to run a JQL Integration task that specifically targets the affected projects and Sub-Task Issue Type.
Run Board Sync should be set to NO.

Here is a sample image of what the JQL Integration would look like

We suggest starting with only one or a few projects to begin with, so that the JQL Integration job doesn't run for hours. That way you can confirm that it is successful before trying other projects.