I had a windows XP and an ubuntu 9.10 on sda and another ubuntu 9.10 and a 
xubuntu installation on sdb. The ubuntu on sdb was my working installation, the 
others were experimental. So I chose to upgrade the working installation 
automatically to 10.4. After the upgrading the windows could not boot. So I 
concluded that the upgrade had moved the boot process from sda2 to sdb1 (where 
the working ubuntu, now 10.4, is), thus rewritten the mbr.
Anyhow, I used windows to rewrite the mbr, after which I had windows, but no 
Ubuntu.
Then I used a Ubuntu-live to install a new GRUB2, after which everything worked 
again.

But I agree that any Ubuntu install or upgrade should offer the option
to skip changing the boot mechanism.

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upgrade karmic to lucid, grub was installed on wrong hd
https://bugs.launchpad.net/bugs/572086
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