Have you ever tried using boot-repair before in an attempt to fix
things? It's the only thing that comes up to mind that might explain
fstab changes. I tested my hunch here and it *does* modify fstab,
commenting things out and re-adding them down the file, especially for
my /boot/efi. I'm not sure why yours would have been picked up by UUID,
though.

In general, this means it might not be an Ubuntu bug at all; the
solution would be to remove the commented out entry for /boot/efi with
the long UUID, and uncomment the short one, which looks to be pointing
to the right partition.

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https://bugs.launchpad.net/bugs/1575813

Title:
  Dual boot does not work after upgrade to 16.04

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