This affects Ubuntu 14.04 64 bit also.  Booting live media off USB2, installing 
to USB3 enclosure, resulted in an empty EFI partition on the target, and the 
new grub.cfg file copied to the host's internal EFI partition, leaving both 
target and host unbootable.
Same machine as above with secure boot disabled, target was a USB3 enclosure 
with a 256G SSD, partitioned with gdisk before the installation was attempted.  
The partitions were:
start             2048  4095        +1M grub-bios
efi                 4096        614399    +300M boot
root1       614400      53043199   +25G
root2   53043200        105471999  +25G
Data  105472000         449404927 +163G
Not formatted before the installation.  At installation, the grub-bios 
partition was unused (just present for future use), and while the efi partition 
was selected as efi, but the format button never became active, and the format 
checkoff never allowed a selection either.  The root1 was selected for the /, 
and the bootloader device was selected as sdc (the target) BECAUSE THE SDC2 
PARTITION was not even a choice (only sdc and sdc3 were choices).  The 
installation finished normally, but had the following problems:
1) target's efi partition was left empty, 
 2) host's efi files were updated, no problem for the .efi loaders, but the 
grub.cfg now used the hd2,gpt3 for the configfile command, which is not present 
after the target is removed.
 3)A NVRAM entry on the host was deleted.  No changes at all were expected on 
the host, and while the removal of the shim boot entry did not cause any 
problems since I had a grubx64 entry also, this unwanted change is an error.
 4) The bootloader for a removable media like USB is not expected to have ANY 
nvram entry, and is expected to be in /EFI/Boot/bootx64.efi.  A properly 
working install to USB should set up the shim or grubx64 that way.
    Easy enough to fix, copy the host's EFI files to the target (they were 
correct for the target after altering the disk number), and restore the host's 
grub.cfg file (I've learned to keep a copy around of the good file).  Or use 
boot-repair I guess, since there are now 214 pages of forum activity there.
  Creating portable Ubuntu systems on USBs should never leave the UEFI  host 
unbootable!

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https://bugs.launchpad.net/bugs/1229488

Title:
  13.10 USB to USB Install on UEFI Secure Boot Machine Left Host
  Unbootable

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