I have two JIRA instances (New, Old ) and both have different configuration, custom fields, issues.
There is a high level description of how you can merge JIRA instances here https://confluence.atlassian.com/jirakb/how-to-merge-jira-applications-instances-244352137.html
Here's a short summary of the steps:
Note that you might face more problems like for example JIRA project import does not properly handle issue history and you might need to manually fix these in the database.
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