Cannot permanently remove boot entry using efibootmgr

Question

My notebook is Lenovo G50-45. I have two dual boot systems Windows 10 and Ubuntu 16.04. I also had Phoenix OS with separate dual boot with Windows 10 (I suppose there is second Grub). I deleted unused system Phoenix via Gparted. Though I cannot delete the efi boot entry. Precisely, I can delete it, but it shows up again after reboot. I used efibootmgr in Linux:

sudo efibootmgr -b 6 -B

In Windows I tried EasyUefi, there it shows even after refresh I do not have to reboot. I do not understand much what is happening by EFI booting. Can someone suggest solution? Here are my current settings:

honza@lenovoG50:~$ sudo efibootmgr -v
BootCurrent: 0004
Timeout: 15 seconds
BootOrder: 0004,0003,2003,0005,0006,0000,2001,2002
Boot0000* Lenovo Recovery System    HD(3,GPT,b11a59bf-42d6-4548-b244-1858af8a20e4,0x276800,0x1f4000)/File(\EFI\Microsoft\Boot\LrsBootMgr.efi)RC
Boot0001* EFI Network 0 for IPv4 (68-F7-28-92-3E-35)    PciRoot(0x0)/Pci(0x2,0x4)/Pci(0x0,0x0)/MAC(68f728923e35,0)/IPv4(0.0.0.0:0<->0.0.0.0:0,0,0)RC
Boot0002* EFI Network 0 for IPv6 (68-F7-28-92-3E-35)    PciRoot(0x0)/Pci(0x2,0x4)/Pci(0x0,0x0)/MAC(68f728923e35,0)/IPv6([::]:<->[::]:,0,0)RC
Boot0003* Windows Boot Manager  HD(2,GPT,c3623e25-a72c-492b-8ff5-9ea449e37436,0x1f4800,0x82000)/File(\EFI\Microsoft\Boot\bootmgfw.efi)WINDOWS.........x...B.C.D.O.B.J.E.C.T.=.{.9.d.e.a.8.6.2.c.-.5.c.d.d.-.4.e.7.0.-.a.c.c.1.-.f.3.2.b.3.4.4.d.4.7.9.5.}....................
Boot0004* ubuntu    HD(2,GPT,c3623e25-a72c-492b-8ff5-9ea449e37436,0x1f4800,0x82000)/File(\EFI\ubuntu\shimx64.efi)
Boot0005* ubuntu    HD(3,GPT,b11a59bf-42d6-4548-b244-1858af8a20e4,0x276800,0x1f4000)/File(\EFI\ubuntu\shimx64.efi)RC
Boot0006* Phoenix OS    HD(2,GPT,c3623e25-a72c-492b-8ff5-9ea449e37436,0x1f4800,0x82000)/File(\EFI\PhoenixOS\Boot\bootx64.efi)WINDOWS.........x...B.C.D.O.B.J.E.C.T.=.{.1.e.a.a.d.8.9.3.-.d.e.d.e.-.1.1.e.7.-.b.f.a.7.-.b.5.e.0.8.c.6.0.2.4.d.f.}....................
Boot2001* EFI USB Device    RC
Boot2002* EFI DVD/CDROM RC
Boot2003* EFI Network   RC

EDIT

I followed advice and after reboot to Windows this is output of EasyUEFI:

Answer 1

When logged into the installed Ubuntu, type the following command, as root, to delete a specific entry:

efibootmgr -b 0006 -B

The number (0006) is the hexadecimal number representing the entry you want to delete.

and type in the terminal:

sudo update-grub

Answer 2

In my case I incorrectly formatted Phoenix OS, it did not do any visible damage, and also did many other attempts and experiment. Surprisingly, I could boot all system I have (Windows 10, ubuntu 16.04). Therefore

1. If your plan is to uninstall Phoenix OS, find proper instructions

(see e. g. my https://superuser.com/questions/1398508/difference-between-easyuefi-boot-item-and-mounted-disk-folder/1398626#1398626 B. paragraph)

2. Removing Phoenix system boot entry, if you incorrectly uninstalled Phoenix OS

a) In ubuntu efibootmgr does not seem to do much. Only check what entries are there by:

 sudo efibootmgr -v

b) In Windows the easiest way comes from:

https://www.youtube.com/watch?v=zyOBF2ePvHY

using bcdedit in admin command prompt: to see all bootable options.

bcdedit /enum all 

There are (usually) many items. So, if you see it for the first time you may get lost. I think the best is to compare it with EasyUEFI outup. See in picture in question:

File path:\EFI\PhoenixOS\Boot\bootx64.efi.

I show small part of my bcdedit /enum all output:

 Firmware Boot Manager
 ---------------------
 identifier              {fwbootmgr}
 displayorder            {1eaad893-dede-11e7-bfa7-b5e08c6024df}
                         {933ae2d3-bf4b-11e4-8258-68f728923e35}
                         {19f0e09b-20f3-11e9-83f9-806e6f6e6963}
                         {c2d01e39-20bc-11e9-83f6-806e6f6e6963}
                         {203b70a1-1fd2-11e9-83f3-806e6f6e6963}
                         {881ea240-bf4f-11e4-8a37-806e6f6e6963}
                         {881ea242-bf4f-11e4-8a37-806e6f6e6963}
                         {881ea23e-bf4f-11e4-8a37-806e6f6e6963}
                         {164f529a-6ec2-11e7-8308-806e6f6e6963}
 timeout                 6

Windows Boot Manager
--------------------
identifier              {1eaad893-dede-11e7-bfa7-b5e08c6024df}
device                  partition=\Device\HarddiskVolume2
path                    \EFI\PhoenixOS\Boot\bootx64.efi
description             Phoenix OS
locale                  en-US
inherit                 {globalsettings}
resumeobject            {933ae2da-bf4b-11e4-8258-68f728923e35}
toolsdisplayorder       {memdiag}
timeout                 0

I did not care about "Windows Boot Manager" important is path for identification. Next you have to copy UUID (=identifier item) {1eaad893-dede-11e7-bfa7-b5e08c6024df}. (It should vary in your case). And delete this entry by:

bcdedit /delete {1eaad893-dede-11e7-bfa7-b5e08c6024df}

I did reboot. But I think it is not necessary. Now, you should not see Phoenix OS boot entry either in EasyUEFI nor by bcdedit /enum all nor in BIOS boot options. That is it.

Answer 3

'Grub Customizer' worked easily for me. I'm running ver. 5.1.1 on Ubuntu 18.04. http://ubuntuhandbook.org/index.php/2016/04/install-grub-customizer-ubuntu-16-04-lts/

After using Boot repair I had multiple Win10 listings in boot two booted correctly into windows two did not. Grub Customizer easily fixed that. You can revert back also.

https://sourceforge.net/p/boot-repair/home/Home/