Please go through the following link for complete details to merge two Jira Server instances: https://confluence.atlassian.com/jirakb/merge-multiple-instances-of-jira-server-244352137.html
In short:
If you want to merge JIRA A into existing JIRA B instance,
Just to add this info as head's up.
If you plan to upgrade from JIRA and JIRA Agile less than 6.4.x and 6.3.5 respectively, you must upgrade to JIRA Software 7.0 as an interim version before upgrading further.
Good luck!
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