updade removes entries from grub menu.lst

I use edgy. I have accepted a couple of updates last few days, but today
I saw that some update has removed the Windows entry from grub's menu.lst,
so I could not dual boot. I have corrected this, but my question is:
Would automatic updates revert my changes to any configfile I have made
so far and would make in future back to default state? Can I somehow
protect my changes? Is there any gentoo's etc-update equivalent? Thanx.