You've run into what I call a "boot coup" -- see this page of the rEFInd documentation for details. You may be able to get rEFInd booting again by typing sudo refind-mkdefault in an Ubuntu Terminal window. If that doesn't work, you could try re-installing rEFInd from either OS X (preferred) or Ubuntu (if necessary). The page referenced earlier provides additional methods of recovery.
Given the order in which you installed software, you may want to install the ext4fs (or whatever filesystem holds your kernel) driver for EFI, as described on the rEFInd drivers page. As it is now, chances are this driver isn't installed, which means rEFInd will boot Ubuntu only via GRUB; but a more direct boot of the kernel is sometimes more reliable and easier to maintain. To do this more direct boot, though, the EFI filesystem driver is required.