rEFInd isn't even part of Ubuntu. From what you describe, efibootmgr is
functioning just fine. You likely need to file a bug against rEFInd
instead.
** Changed in: efibootmgr (Ubuntu)
Status: New => Invalid
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https://bugs.launchpad.net/bugs/1413943
Title:
Upgrading to vivid breaks dual boot on OS X
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