When you select either 'Disinfect' or 'Delete' from the SBAV CD menu you see the following message:
The disk is marked 'in use'. Probably Windows was not shut down correctly. Your options are:
[Recommended] Return to Windows and shut it down correctly.
Proceed with the scan at your own risk. This may result in disk corruption. If in doubt, contact Sophos Technical Support.
First seen in
Sophos Bootable Anti-Virus
Your computer was not shut down properly.
What To Do
If you proceed with the scan on a computer that was not shutdown properly and has an NTFS hard disk, the hard disk will not be checked by the Windows disk utility and any disinfection or deleting that the SBAV performs could cause even more damage.
Once the scan is complete, you should perform a Windows Disk Integrity check on the computer as soon as possible to repair any damage.