rEFind doal boot option disappeared after ubuntu 14 to 16 upgrade

You've encountered what I call a boot coup -- the update from Ubuntu 14[.04?] to 16[.04?] has made GRUB the default boot manager, bypassing rEFInd. rEFInd is probably still installed and can be made the default again in several ways, or there are other things you might do:

• Use refind-mkdefault -- This script, which comes with rEFInd, will probably fix the problem. If you installed rEFInd in OS X, it won't be in the path from Ubuntu, so you'd need to find it on your OS X partition or obtain a version in Ubuntu. The most direct way is to download it from rEFInd's Sourceforge repository.
• Use efibootmgr -- You can type sudo efibootmgr -v to see all your boot options and the current boot order (the BootOrder line). If you can figure out which option is rEFInd (it probably refers to refind_x64.efi), you can then change the boot order with the -o option, as in sudo efibootmgr -o xxxx[,yyyy,zzzz], where xxxx is the Boot#### option for rEFInd and subsequent numbers refer to alternative boot options. This is what refind-mkdefault does; the script just does it automatically.
• Use bless -- If you can boot to OS X (by using Alt or Option as you power on the computer), you can use the bless utility in OS X to restore rEFInd as the main boot program. You'd follow steps 1, 2, and 8 in the manual rEFInd OS X installation procedure. Note that, if you're using a recent version of OS X, you might run into problems with SIP.
• Re-install rEFInd -- You could install the rEFInd PPA or Debian package in Ubuntu; or use the Alt or Option key as you power on the computer to do a one-time boot to OS X and re-install rEFInd there. This option is overkill, and so might accidentally make a change you don't intend, but it can be relatively easy. On Macs, I recommend doing the re-installation from OS X if possible, although you might run into issues with SIP.
• Keep using GRUB -- Presumably GRUB is controlling the boot process now. In theory, it should show you a boot menu that will enable booting either Ubuntu or OS X; however, it's not clear from your description if that's the case. If not, or if the OS X option doesn't work, GRUB Customizer might help you get it working better.

Your personal preferences and skill level come into play, but overall, I'd say you should try these options in more-or-less the order noted.