The SQL for JIRA plugin might help as it allows to connect to JIRA remotely via JDBC. It also supports JIRA JQL embedded in SQL queries, therefore you would be able to connect to both JIRA instances from a single point and fetch data from each instance in order to compare them without too much effort.
It supports standard SQL without too much constraints as well as any JIRA JQL query regardless its complexity, so you could filter data in a really powerful and straightforward way.
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