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This is a special case that needs a slightly different approach in most cases. Delete errors can occur if you have subtasks in your project since when an issue gets deleted, it deletes its subtasks, but the subtasks may still be in the list to process. They will generate not found errors when they get processed. So, for delete processing, use JQL that includes issuetype in standardIssueTypes(). If trying to delete all issues in a project, don't use the shortcut way of just using --project, but use JQL instead.