Aloha from the Big Island,
I am using a dual boot system with Win 7 and Suse 11.4. I have experienced this problem before with XP and an earlier version of Suse. Fortunately Suse has a repair feature that will allow you to recover an installed system. I don't know if Ubuntu has that feature but I have been disappointed by other Ubuntu features so I stick to Suse.
You are correct that once you instal windoze the linux boot loader will disappear. If you do a reinstall of Ubuntu (perhaps an upgrade) after a Windows install you should get the boot loader back and it will recognize the windows installation as well. Of course you must back up your home partition but you likely have done that already. Also if you partition the hard drive before you install Windoze it won't mess with anything else but the partition you give it.
Suse does not overwrite the home partition unless you ask it to. I'm not familiar with the Ubuntu configuration tool that allows you to change boot loader settings. In Suse it is Yast - a very full featured services tool that is quite easy to use and almost flawless.
If I were you I'd try this an a machine that is of little consequence.
Good Luck
Tarael