I would like to know if there is any way to make backup of Jira (Projects, workflows etc.) without copying issues. I would like to have everything the same in next Jira instance, but without issues.
No you can't exclude issues from a backup. But you could restore a full system back on your new instance and then delete all the issues.
Try this plugin ;
https://marketplace.atlassian.com/apps/1211611/configuration-manager-for-jira?hosting=server&tab=overview
Not sure if it satisfies your requirement.
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