This bug has been fixed in hardy, in grub version 0.97-29ubuntu7 and
above:
grub (0.97-29ubuntu7) hardy; urgency=low
* debian/update-grub: use ucf to record changes to the autogenerated
kernel list
It is still advisable that boot options for other operating systems such
as Windows be added outside the "automagic kernels list" markers, but
going forward users will receive a debconf warning from update-grub if
the update will overwrite local changes.
** Changed in: grub (Ubuntu Hardy)
Importance: Medium => High
Status: Confirmed => Fix Released
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Default update-grub behaviour is not intuitive with respect to user
modifications
https://bugs.launchpad.net/bugs/21412
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