Pick one of them to keep, and install the other application on to it (For example, if you have myjsoftware.atlassian.net and myjsd.atlassian.net, and you wanted to keep myjsoftware.atlassian.net, then you would add Jira Service Desk to it)
Then there's the hard bit - you'll probably want to merge stuff from the one you are dropping into the other one.
Merging Jira systems is not a simple thing to do, whatever the platform you're on. What appetite do you have for merging? Would you need all the projects? Or just a couple?
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