Comment 3 for bug 1518495

I have the same problem on Manjaro Linux. Deleting the placeholders from submenues, as Daniel had recommended, doesn't help. Moreover when the placeholders are within submenues in FULL (not customized) configuration, it doesn't make any trouble in saving the configuration. Problems start when I want to delete this submenu items from the main boot menu.

Here is my grub.cfg.new file.

#
# DO NOT EDIT THIS FILE
#
# It is automatically generated by grub-mkconfig using templates
# from /etc/grub.d and settings from /etc/default/grub
#

### BEGIN /etc/grub.d/00_header ###
insmod part_gpt
insmod part_msdos
if [ -s $prefix/grubenv ]; then
  load_env
fi
if [ "${next_entry}" ] ; then
   set default="${next_entry}"
   set next_entry=
   save_env next_entry
   set boot_once=true
else
   set default="${saved_entry}"
fi

if [ x"${feature_menuentry_id}" = xy ]; then
  menuentry_id_option="--id"
else
  menuentry_id_option=""
fi

export menuentry_id_option

if [ "${prev_saved_entry}" ]; then
  set saved_entry="${prev_saved_entry}"
  save_env saved_entry
  set prev_saved_entry=
  save_env prev_saved_entry
  set boot_once=true
fi

function savedefault {
  if [ -z "${boot_once}" ]; then
    saved_entry="${chosen}"
    save_env saved_entry
  fi
}

function load_video {
  if [ x$feature_all_video_module = xy ]; then
    insmod all_video
  else
    insmod efi_gop
    insmod efi_uga
    insmod ieee1275_fb
    insmod vbe
    insmod vga
    insmod video_bochs
    insmod video_cirrus
  fi
}

set menu_color_normal=light-gray/black
set menu_color_highlight=green/black

if [ x$feature_default_font_path = xy ] ; then
   font=unicode
else
insmod part_gpt
insmod ext2
set root='hd0,gpt3'
if [ x$feature_platform_search_hint = xy ]; then
  search --no-floppy --fs-uuid --set=root --hint-ieee1275='ieee1275//disk@0,gpt3' --hint-bios=hd0,gpt3 --hint-efi=hd0,gpt3 --hint-baremetal=ahci0,gpt3 9bda84fb-5b33-4f8d-a574-240ade54186c
else
  search --no-floppy --fs-uuid --set=root 9bda84fb-5b33-4f8d-a574-240ade54186c
fi
    font="/usr/share/grub/unicode.pf2"
fi

if loadfont $font ; then
  set gfxmode=auto
  load_video
  insmod gfxterm
  set locale_dir=$prefix/locale
  set lang=uk_UA
  insmod gettext
fi
terminal_input console
terminal_output gfxterm
insmod part_gpt
insmod ext2
set root='hd0,gpt3'
if [ x$feature_platform_search_hint = xy ]; then
  search --no-floppy --fs-uuid --set=root --hint-ieee1275='ieee1275//disk@0,gpt3' --hint-bios=hd0,gpt3 --hint-efi=hd0,gpt3 --hint-baremetal=ahci0,gpt3 9bda84fb-5b33-4f8d-a574-240ade54186c
else
  search --no-floppy --fs-uuid --set=root 9bda84fb-5b33-4f8d-a574-240ade54186c
fi
insmod gfxmenu
loadfont ($root)/usr/share/grub/themes/manjaro/dejavu_sans_12.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/dejavu_sans_14.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/dejavu_sans_16.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/dejavu_sans_24.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/dejavu_sans_48.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/dejavu_sans_bold_16.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/dejavu_sans_mono_12.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-12.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-14.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-16.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-18.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-b12.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-b14.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-b16.pf2
loadfont ($root)/usr/share/grub/themes/manjaro/terminus-b18.pf2
insmod png
set theme=($root)/usr/share/grub/themes/manjaro/theme.txt
export theme
if [ x$feature_timeout_style = xy ] ; then
  set timeout_style=menu
  set timeout=5
# Fallback normal timeout code in case the timeout_style feature is
# unavailable.
else
  set timeout=5
fi
### END /etc/grub.d/00_header ###

### BEGIN /etc/grub.d/01_menu_auto_hide ###
if [ "${boot_success}" = "1" -o "${boot_indeterminate}" = "1" ]; then
  set last_boot_ok=1
else
  set last_boot_ok=0
fi

# Reset boot_indeterminate after a successful boot
if [ "${boot_success}" = "1" ] ; then
  set boot_indeterminate=0
# Avoid boot_indeterminate causing the menu to be hidden more then once
elif [ "${boot_indeterminate}" = "1" ]; then
  set boot_indeterminate=2
fi
set boot_success=0
save_env boot_success boot_indeterminate

if [ x$feature_timeout_style = xy ] ; then
  if [ "${menu_show_once}" ]; then
    unset menu_show_once
    save_env menu_show_once
    set timeout_style=menu
    set timeout=60
  elif [ "${menu_auto_hide}" -a "${last_boot_ok}" = "1" ]; then
    set orig_timeout_style=${timeout_style}
    set orig_timeout=${timeout}
    if [ "${fastboot}" = "1" ]; then
      # timeout_style=menu + timeout=0 avoids the countdown code keypress check
      set timeout_style=menu
      set timeout=0
    else
      set timeout_style=hidden
      set timeout=1
    fi
  fi
fi
### END /etc/grub.d/01_menu_auto_hide ###

### BEGIN /etc/grub.d/10_linux_proxy ###

menuentry "Manjaro Linux" --class manjaro --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-simple-9bda84fb-5b33-4f8d-a574-240ade54186c' {
 savedefault
 load_video
 set gfxpayload=keep
 insmod gzio
 insmod part_gpt
 insmod ext2
 set root='hd0,gpt3'
 if [ x$feature_platform_search_hint = xy ]; then
   search --no-floppy --fs-uuid --set=root --hint-ieee1275='ieee1275//disk@0,gpt3' --hint-bios=hd0,gpt3 --hint-efi=hd0,gpt3 --hint-baremetal=ahci0,gpt3 9bda84fb-5b33-4f8d-a574-240ade54186c
 else
   search --no-floppy --fs-uuid --set=root 9bda84fb-5b33-4f8d-a574-240ade54186c
 fi
 linux /boot/vmlinuz-4.19-x86_64 root=UUID=9bda84fb-5b33-4f8d-a574-240ade54186c rw quiet resume=UUID=154f91a7-0e28-42f4-a498-478a390ebead
 initrd /boot/intel-ucode.img /boot/initramfs-4.19-x86_64.img
}
### END /etc/grub.d/10_linux_proxy ###

### BEGIN /etc/grub.d/20_linux_xen ###
### END /etc/grub.d/20_linux_xen ###

### BEGIN /etc/grub.d/30_os-prober_proxy ###

# Other OS found, undo autohiding of menu unless menu_auto_hide=2
if [ "${orig_timeout_style}" -a "${menu_auto_hide}" != "2" ]; then
  set timeout_style=${orig_timeout_style}
  set timeout=${orig_timeout}
fi
menuentry "Windows Boot Manager (on /dev/sda1)" --class windows --class os $menuentry_id_option 'osprober-efi-50EE-A38C' {
 savedefault
 insmod part_gpt
 insmod fat
 set root='hd0,gpt1'
 if [ x$feature_platform_search_hint = xy ]; then
   search --no-floppy --fs-uuid --set=root --hint-ieee1275='ieee1275//disk@0,gpt1' --hint-bios=hd0,gpt1 --hint-efi=hd0,gpt1 --hint-baremetal=ahci0,gpt1 50EE-A38C
 else
   search --no-floppy --fs-uuid --set=root 50EE-A38C
 fi
 chainloader /EFI/Microsoft/Boot/bootmgfw.efi
}
menuentry "Linux Mint 19.1 Tessa (19.1) (on /dev/sda6)" --class linuxmint --class gnu-linux --class gnu --class os $menuentry_id_option 'osprober-gnulinux-simple-273e6d8a-820e-4944-8c32-291be1db7d8a' {
 savedefault
 insmod part_gpt
 insmod ext2
 set root='hd0,gpt6'
 if [ x$feature_platform_search_hint = xy ]; then
   search --no-floppy --fs-uuid --set=root --hint-ieee1275='ieee1275//disk@0,gpt6' --hint-bios=hd0,gpt6 --hint-efi=hd0,gpt6 --hint-baremetal=ahci0,gpt6 273e6d8a-820e-4944-8c32-291be1db7d8a
 else
   search --no-floppy --fs-uuid --set=root 273e6d8a-820e-4944-8c32-291be1db7d8a
 fi
 linux /boot/vmlinuz-4.15.0-43-generic root=UUID=273e6d8a-820e-4944-8c32-291be1db7d8a ro quiet splash $vt_handoff
 initrd /boot/initrd.img-4.15.0-43-generic
}
### END /etc/grub.d/30_os-prober_proxy ###

### BEGIN /etc/grub.d/40_custom ###
# This file provides an easy way to add custom menu entries. Simply type the
# menu entries you want to add after this comment. Be careful not to change
# the 'exec tail' line above.
### END /etc/grub.d/40_custom ###

### BEGIN /etc/grub.d/41_custom ###
if [ -f ${config_directory}/custom.cfg ]; then
  source ${config_directory}/custom.cfg
elif [ -z "${config_directory}" -a -f $prefix/custom.cfg ]; then
  source $prefix/custom.cfg;
fi
### END /etc/grub.d/41_custom ###

### BEGIN /etc/grub.d/42_grub-customizer_menu_color_helper ###
### END /etc/grub.d/42_grub-customizer_menu_color_helper ###

### BEGIN /etc/grub.d/60_memtest86+_proxy ###

if [ "${grub_platform}" == "pc" ]; then

fi
### END /etc/grub.d/60_memtest86+_proxy ###

### BEGIN /etc/grub.d/61_linux_proxy ###
### END /etc/grub.d/61_linux_proxy ###

### BEGIN /etc/grub.d/62_os-prober_proxy ###
### END /etc/grub.d/62_os-prober_proxy ###