Hello MihailsSvetlovs,
You can't stop the merging process of the 2 checkpoints as the Hyper V will automatically execute it once you delete the checkpoints. As an alternative, you can try freeing up space where the .VHDX file located, as this might help you out better.
But if you are unable to free up the space from the respected drive then try the below link to use Storage Migration
using Virtual Machine Storage Migration Overview,
https://learn.microsoft.com/en-us/previous-versions/windows/it-pro/windows-server-2012-R2-and-2012/hh831656(v=ws.11)
Hyper-V in Windows Server 2012 introduces support for moving virtual machine storage without downtime by making it possible to move the storage while the virtual machine remains running. You can perform this task by using a new wizard in Hyper-V Manager or by using new Hyper-V cmdlets for Windows PowerShell.
You can add storage to either a stand-alone computer or to a Hyper-V cluster, and then move virtual machines to the new storage while the virtual machines continue to run.
Hope this answers all your queries, if not please do repost back.
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