were you successful with uninstalling and re-installing?
I got a similar issue here: we have JIRA 6.1. on our test system and want to downgrade to 5.2.6 (our production-version), as we want to test the upgrade to the latest version.
According to the comments here it would be the best to uninstall and install the old version. I could then restore a application- and database-backup from our previous 5.2-test system - and it should work then. Right?
Short answer is "no".
There's several docs about downgrading Jira floating around the web, and they have two important points - first they're all very old, and secondly, even then, they say "Do not do this (but if you must...)
In theory, of course, it is possible. The best route is probably to export the 6.1 data to xml, work out what needs to be migrated back to the previous format, change the xml and then import it into the previous version. You could probably do it directly in the database as well.
But whatever route you think is best, it is a LOT of work. Which gets potentially exponentially more difficult with each type of custom field you use, each plugin you're using and with each version of Jira you diverge by.
I've only ever successfully downgraded a Jira install three times. Once from 5.0.4 to 5.0.2, and the other two don't really count because I was able to simplify them by deleting all the issues.
I suspect a better route would be to hassle Zephyr to make it compatible with Jira 6.1
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