Structure data is stored separately from JIRA data. See https://wiki.almworks.com/x/OgBg
Basically, if both instances are down (or if you have Structure plugin temporarily disabled on both), you can just copy structure/ sub-directory from JIRA home.
Otherwise, you need to do Administration | Structure | Backup Structure and Restore Structure.
Hope this helps!
Sorry, I need to know what the method was. Did you use Jira's export and import? A flat database dump and reload? Restored a database backup? Something else?
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