Comment # 5 on bug 1161248 from Jiri Srain

The current behavior is correct: There is no way to change the menu with
current GRUB, the only thing you can do is to re-generate it. This is by
design.

In default configuration, you do not have any custom section, but probe for
operating systems in other partitions. If you re-generate the boot menu and
some of the partitions are not accessible, you are out of luck.

If you don't like this behavior, the only option (Michael, correct me) is:

- disable OS prober in /etc/default/grub

- write the sections of the other systems (which should be permanent) into
/etc/grub.d/40_custom and re-generate the GRUB menu. Then they will remain
permanent

The boot configuration file is more like a script - there are no tools editing
it, but only generating from scratch. A part of generating it is processing
files from /etc/grub.d, where you can put your own piece of code.

As I wrote, the behavior is as designed. You may even notice that e.g. the YaST
module does not even have the option to edit bootloader sections, exactly from
this reason.