Are the applications hosted on the same Jira instance or linked together by an application link? If they are then you can just create a new project on the Jira Service Desk server and simply move the issues to the new project.
If they are not and they are separate instances you will have to follow these instructions. https://confluence.atlassian.com/adminjiraserver/restoring-a-project-from-backup-938847691.html
You can set them up on different servers and it will still work. You will have the benefit of being able to use apps on JSD and not have to purchase the license for all of your server licenses. We ended up putting ours on the same instance because it is easier to manage updates, users, etc because you only have to do it for one. There are pros and cons to both setups. It really just depends on what you are trying to do as a business.
@Rick ONeill Sorry that was my bad I forgot that we configuration manager for Jira. had https://marketplace.atlassian.com/apps/1211611/configuration-manager-for-jira?hosting=server&tab=overview
You can install and use free for 30days or purchase to have the functionality forever moving forward. I apologize as I forgot that we purchased this. The application link will allow you to link issues but will not allow you to move issues between instances.
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