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I have a "test all the operating systems"-laptop which was running Windows and Ubuntu MATE, with rEFInd used as boot manager.

Yesterday I installed Qubes on the last third of the drive. I've since read why you should not but for just testing the OS I would still not mind doing it.

Unfortunately I can no longer boot the old OS:es. Neither rEFInd. After some reading I guess Qubes is legacy-boot only, but why that has completely broken my UEFI-booting the old systems I do not know.

Qubes installation of grub boots fine, but if I try to launch rEFInd from it it fails:

grub> ls
(hd0) (hd0, gpt10) (hd0, gpt9) (hd0, gpt8) (hd0, gpt7) (hd0, gpt6) (hd0, gpt5) (hd0, gpt4) (hd0, gpt3) (hd0, gpt2) (hd0, gpt1)
grub> chainloader (hd0,gpt3)/efi/Boot/bootx64.efi
error: invalid signature

Manually trying to select the efi-files from the computers firmware fails, the mouse even hangs when the firmware tries to list available efi-files from the hard drive.

Booting rEFInd installed on a thumb drive works fine, so I conclude the firmware on the machine is intact, but the hard drive got messed up by the Qubes installer.

What did it do to my drive? How can I restore it?

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Looking at the drive with gdisk renders:

root@ubuntu-mate:~# gdisk /dev/sda
GPT fdisk (gdisk) version 1.0.1

Partition table scan:
  MBR: protective
  BSD: not present
  APM: not present
  GPT: present

Found valid GPT with protective MBR; using GPT.

Command (? for help): v

Warning: The 0xEE protective partition in the MBR is marked as active. This is
technically a violation of the GPT specification, and can cause some EFIs to
ignore the disk, but it is required to boot from a GPT disk on some BIOS-based
computers. You can clear this flag by creating a fresh protective MBR using
the 'n' option on the experts' menu.

No problems found. 2925 free sectors (1.4 MiB) available in 2
segments, the largest of which is 2014 (1007.0 KiB) in size.

Following the instructions from gdisk:

Command (? for help): ?   
b   back up GPT data to a file
c   change a partition's name
d   delete a partition
i   show detailed information on a partition
l   list known partition types
n   add a new partition
o   create a new empty GUID partition table (GPT)
p   print the partition table
q   quit without saving changes
r   recovery and transformation options (experts only)
s   sort partitions
t   change a partition's type code
v   verify disk
w   write table to disk and exit
x   extra functionality (experts only)
?   print this menu

Command (? for help): r

Recovery/transformation command (? for help): ?
b   use backup GPT header (rebuilding main)
c   load backup partition table from disk (rebuilding main)
d   use main GPT header (rebuilding backup)
e   load main partition table from disk (rebuilding backup)
f   load MBR and build fresh GPT from it
g   convert GPT into MBR and exit
h   make hybrid MBR
i   show detailed information on a partition
l   load partition data from a backup file
m   return to main menu
o   print protective MBR data
p   print the partition table
q   quit without saving changes
t   transform BSD disklabel partition
v   verify disk
w   write table to disk and exit
x   extra functionality (experts only)
?   print this menu

Recovery/transformation command (? for help): x

Expert command (? for help): ?
a   set attributes
c   change partition GUID
d   display the sector alignment value
e   relocate backup data structures to the end of the disk
g   change disk GUID
h   recompute CHS values in protective/hybrid MBR
i   show detailed information on a partition
l   set the sector alignment value
m   return to main menu
n   create a new protective MBR
o   print protective MBR data
p   print the partition table
q   quit without saving changes
r   recovery and transformation options (experts only)
s   resize partition table
t   transpose two partition table entries
u   replicate partition table on new device
v   verify disk
w   write table to disk and exit
z   zap (destroy) GPT data structures and exit
?   print this menu

Expert command (? for help): n

Expert command (? for help): w

Final checks complete. About to write GPT data. THIS WILL OVERWRITE EXISTING
PARTITIONS!!

Do you want to proceed? (Y/N): Y
OK; writing new GUID partition table (GPT) to /dev/sda.
Warning: The kernel is still using the old partition table.
The new table will be used at the next reboot or after you
run partprobe(8) or kpartx(8)
The operation has completed successfully.

Reboot and I'm greeted by rEFInd again! Qubes won't boot any more of course.

Seems the protective mbr created by Qubes was the problem.

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  • 1
    Thanks so much! I spent almost a whole day trying to figure out why the Qubes installer broke my existing UEFI setup. These instructions fixed the problem. – Josh Haberman Dec 31 '18 at 5:02

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