Preserving boot camp option after re-installing Mac OS X

I have a 1st gen Mac Pro with Vista installed on a second hard drive under boot camp. Recently for reasons that I can't find a solution to, my machine has become rather unstable with numerous crashes and lockups that never used to happen.
I want to do a clean reinstall of Mac OS, but I'm concerned that this will replace the boot sector on the main disk and might remove the option to boot into Vista, meaning the Microsoft OS will still be installed but I'll have no way of accessing it.
Has anyone reinstalled Mac OS and managed to keep the boot camp option? Does it get wiped out? If so, what I can I do to get it back. I don't really want to install Vista again as well.

If you are worred: pull 2nd drive out, backup both Vista and OS X.
If you are haviing trouble, run Disk Warrior regularly, and make some backup clones with SuperDuper.
As for OS X, Apple has some troubleshooting OS X articles, and lots of help in the OS X Leopard forums.
And no, this isn't the same as XP and dealing with boot.ini but you might at worst have to boot from Vista DVD once at worst.

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