Boot and system Drives are on different partitions

I need to convert an existing Windows Server 2003 Standard Service Pack 2 to a virtual server. I have converted a few servers with Xenconvert and the free version of Xenserver. It states in the users guide that "XenConvert can only convert a workload from a source machine on which the system drive is the same as the boot drive. For example, boot.ini and the \Windows must both reside on C:".

Now the problem is that the OS is on the E: drive which is on the same disk but a separate partition. The E: drive is NTFS on a logical drive. The C: drive contains the boot.ini files. It is only 2GB in size, a primary partition, and a FAT partition.

Is there any way to get them both on the same partition without loosing the OS, programs, and data from the E: drive or the programs and data from C:?

I did not install this server!!!
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More about boot system drives partitions
  1. There is no way to move the system files on an NT based OS without reinstalling. There are just TOO many references to full paths in the registry.

    However, you should be able to perform the conversion to virtual drives manually, which is a pain, but better than reinstalling/reconfiguring the server. And you will need to make sure the drive letter remain the same.
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