There will be asked if you want to keep your our grub file or the proposed one by the package distributor. Take the last choice but only after you have saved your old copy of the menu.lst as for instance menu_old.lst so that you can adapt the automatically renewed menu.lst to its former state with its renewals of the new krnel incorporated of course, but with the adaptions you made mostly to suit your own special setup on more partitions.
Do it right away before you reboot or else you will probalbly have great trouble rebooting! In terminal (or open your file manger as root)
sudo gedit /boot/grub/menu.lst
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