I still use the Hyper-V console to do some stuff because I find it suits me from time to time, despite having VMM 2008. One of these is disk management on the cluster because you can’t remotely manage files on a GUID drive. I just did some work on a VHD and went back to VMM to add some SCSI disks. However, my boot VHD, an IDE disk was gone, disappeared, vamoose!
I tried a few things (checking the file location in Hyper-V MMC, refreshing the host and migrating the VM) but the fix was to make a simple alteration to the VM configuration in VMM. I added a SCSI controller and saved the changes. The disk reappeared. Note: The disk was there. Starting the machine up may have popped it back in VMM (I was in the process of deploying and customising). I know for certain that Hyper-V knew it was there and the machine would have booted OK.