Thanks for your response.That's what I'm afraid of.
A couple of consideration why I raised this question.
1. If we don't have an option for partial backup it also means there's no option for partial retrieval. So if someone with proper rights deleted one project and it needs to be restored, everything from the last backup will be restored so activities and changes made after the last backup will be overwritten.
2. If the reason for archiving JIRA is to free up disk space/storage, then everything from Day 1 up to present will be archived. Project and Issues that we want to maintain in JIRA will not be kept and will be archived.
One way of archiving JIRA issues is exporting those to indeable, searchable PDF documents with the JIRA PDF View Plugin. As this plugin can generate documents from the result set of any JIRA query (and filter), you can archive issues by dates, projects, users, and generally any other criteria supported by JQL.
You can export either one PDF file containing many issues, or one PDF per issue, whichever fits your needs better. You can even automate the process using the PDF Automation Plugin or the PDF API. Then put those documents into a Document Management System (like Alfresco) and you are done.
There is also a related public feature request Archiving old issues, please see Atlassian's official statement there: https://jira.atlassian.com/browse/JRA-5843
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