Not that this is in anyway definitive (yet!), but the connector suite that we have been developing here at CustomWare, integrating JIRA with Zendesk (and many others), is designed to work with the NetworkedHelpDesk.org APIs.
It is in fact more powerful than just those APIs allow for, able to directly use the JIRA API if needed.
With some modification, it is not hard to imagine connecting two JIRA instances with the connector, and if the need is great it might well happen. The structure is definitely there to make this happen.
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