I have seen this happen a few times and i really hate how the checkpoint / snapshot feature works in Hyper-V. Basically it creates an “.avhd” file for each snapshot you create and using an “.xml” file keeps track of how they are stitched together. I had a customer that had a disk failure. and after rebuilding the host, i was lucky enough that the partition the VHD files lived on was intact. What really bothers me is the fact that you can’t simply import the virtual machine. The reason is quite silly: it was not exported. In order to get the vm back online you must use the Disk Editor and merge the files back into the root file one at a time. pretty lame microsoft.
Here is how you do it.
1) start by backing up the folder before you start
2) rename all the avhd files in the snapshot folder to vhd. (but first write down the modified date and time.
3) open the Disk editor in hyper-v manager and merge the most recent file to the parent
4) repeat this process until you have no more snapshots left.
For more reading on this subject, head on over to technet: