Taking whole backup of your Jira, if not already configured as a service is probably the best way to do it. It will ensure all the configurations and data are backed up, of course for whole instance. It is also possible to restore individual project from the backup which only works when all the required configurations are already there in your instance.
This is of course the xml backup of Jira instance. Ideally you should also have backup policy for your database and file system.
You can also export individual project issues to csv.
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