Windows installer will deleted my files on a USB disk

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I have a USB disk with my 'working directory' on it to create an unattended install. The directory is on the root of the disk and is called Windows.

After trying my disc on my real hardware (not in a virtual pc) the installer asked if I wanted to delete the current windows install. I answered yes, I thought it meant the install on C:\

But when it was ready it had wiped the Windows directory on my USB disk!

I never got the screen where you can select the disk to install onto, but i did get that screen every time i tried in Virtual PC.

Just wanted to tell you all this, if anyone has similar experience, or can explain the way the installer chooses the destination disk, I'd love to hear.

Thanks!