Atlassian support got back to me very quickly on this.
The cause was somehow a duplicate isue type of Epic was created (not sure how but probably related to the very customised workflow I had to create recently).
Once this duplicate issue type was deleted order was restored to JIRA and the Agile boards.
Can you try a full reindexing and see if that helps? Also, check the logs for any errors.
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Tried multiple full locked reindexes and still not appearing.
I continued to import my stories and used the Epic link field populated with the relevent Epic JIRA key and they have imported correctly with the links intact.
So the same issues still remain of:
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Can you check if the Epics and the other issues satisfies the board filter criteria? Check under Board configuration > General > Filter query
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The filter is the default one: project = MALV ORDER BY Rank ASC
also by clicking this link under configure I get a result set with all my Epics.
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Also after troubleshooting further. All of my existing projects are now missing their epics from the Board. Furthermore I can't link any new stories to any Epics. I get no matches found even when I use the name and ID.
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