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Vista to 7 Upgrade Files Question

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Question: When upgrading from Windows Vista to Windows 7 Home Premium does the installation replace ALL system files or just the ones are necessary (new)?

If necessary I will next be posting in the Virus ... forum but here is a synopsis of my problem. I have AVG Security Suite v9 installed and it is picking up an instance of Rootkit-Pakes.U I have also checked using Malwarebytes, XoftSpy,and SUPERAntiSpyware with clean reports from all. The problem exists in the atapi.sys file and I know others have had the same problem.

Could it be a false positive?

I don't want to upgrade if the Pakes.U is actually present and if it could be carried over to the new OS installation hence the original question. I know I can do a clean install but don't really want to if I don't have to.

Thoughts appreciated
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