I see, that is similar to the method that Dell uses for it powervault systems, thought I can quite understand Dell mind on that yet, since the programs you install won't be installed in both.
The end result is that if you have a problem, you end up having to reinstall the needed programs before being able to anything else. But that is another story.
For what you are trying to acomplish I think that the easiest way would be to do an image of the OS in the clean state. Then if you need to restore the system you can isntall that image in the other drive.
Now
Let me confirm: You have no problem running duplicate OS's on two different partitions? And you don't use "partition magic" or one of the other boot-loader programs? Presumably you install the two OSs, as I do, by disconnecting one of the drives and installing on the other?
Yes, I have no problem running duplicate OS (it is even the same version) in 2 different partitions, and I don't use any boot loader.
No, I didn't install the OS like that. I never disconnected any of the drives when I installed the other OS. Actually, you can't disconnect logical drives
What I did was:
I installed XP pro in the drive with letter C, then I installed the OS in the drive with letter E (since the partition was made after the set up, the CD-ROM has letter D).
Now, what I was trying to do was to fix a problem with the OS in drive C, it didn't fix when I did the reinstall and that is why I installed in E, so I could at least use the PC for a few days.
Then I erased the WINDOWS folder in C, and reinstalled Xp in C, so now when I boot the computer I have the OS choice to load WINDOWS XP Profesional or WINDOWS XP Profesional, but the first is on C drive, the second in E drive.
Does it make sense??
I just exlained all the process that I did, just to show I didn't use anythin extra. It is not needed to delete the windows folder. I was just trying to fix a previous problem, but I didn't have time to work on it, so I install another copy of the OS in the other drive, so I could pass by a couple of weeks. This was my computer at work, not home, so I had less time to play around. Otherwise I would never installed a seocnd OS even.
Now, there si 2 bad point of having 2 XP OS (or 2 MS OS for that matter).
One, if the OS is the same, it is more likely that it is dead space, because you will only work with one.
You will be able to switch fast to the other OS in case you need it, but it will be as a brand new OS, so havng an image is a lot better.
The other bad point is that you can still access the system files for that OS, so you might accidentally delete files, or progrmas might use the incorrect folder, depending of which OS you are using. At least different OS have different files version.