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Hello, could you please help investigate/fix this issue
@Vijay Uskamalla Jira Align won't automatically delete the story unless you have the Delete Item Status configured under Admin - Jira Settings - Jira Setup. If you have this field configured, then when you delete in Jira, it will also permanently delete in Jira Align.
If you don't want it to immediately permanently delete in Jira Align, then this field is left blank, and you have to go to Admin - Jira Management - Jira Deleted Issues. You have to run this (I would recommend you don't run this during peak times since this is API intensive) and it will provide you a list of all the items that have been deleted in Jira, and then you can decide how you would like to handle it in Jira.
More info about Delete Item Status field: https://help.jiraalign.com/hc/en-us/articles/115000088453
More info about Jira Deleted Issues: https://help.jiraalign.com/hc/en-us/articles/360018815534