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I'm running Hyper-V in Win10 Pro.

The original VHDX file is 4 MB, and I install Win Server 2016 into my instance, which brings the AVHDX file to over 10 gigs.

I want to merge my checkpoint, but when I delete the checkpoint, the AVHDX file gets deleted without merging the changes into the hard disk image VHDX file.

What could I be doing wrong in getting my changes merged in the VHDX file?

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Unless you plan on using checkpoints, best to disable it before starting the VM:

  • VM Settings > Checkpoints - Ensure box for Enable checkpoints is unticked > OK

To merge checkpoints:

  1. Highlight VM > Edit Disk..
    1. Location: (select applicable AVHDX file)
    2. Merge
    3. To the parent virtual hard disk || To new virtual hard disk
    4. Finish
  2. VM Settings > Hard Drive - Virtual Hard Disk: (select the merged VHDX) > OK
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From what you describe it looks like you're doing it correctly, if your only checkpoint is the one prior to installing Windows server. To be certain, be sure you select the very first checkpoint (that was perahsp created automatically), and delete checkpoint sub-tree, and that should merge all changes into the vhdx. It will take a while.

Example of checkpoint tree

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