I agree with Elise, the capabilities your describing of this malware seem not only highly unlikely but are in actual fact impossible. Referring to "virtual machines", I assume you are referring to a piece of malware acting as a hypervisor in the style of something like Blue Pill? Again this kind of rootkit technology is hardware dependent as is any kind of BIOS infection (MBR infection is a different matter however, this could be what you're referring to).
It is possible for a piece of malware to restore itself using chkdsk by marking the part of the file system it resides on as damaged/re
