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I've been trying to figure this out now for sometime, but haven't found an answer.

I have a Server 2016 VM running on HyperV Server 2016.

It has a file storage VHDX formatted as NTFS that is sitting on a mirrored storage spaces virtual disk running ReFS.

Will the files on the VHDX have the benefits of the file integrity streams or would I need to do REFS on both the storage spaces and the VHDX?

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VHDX file itself validates and maintains data integrity using checksums on top of the ReFS. If you would like to have such possibility for independent files, you need to format hard disk as ReFS inside the VM. Moreover, ReFS can still auto-detect data corruption and automatically perform needed repairs without using Storage Spaces.

Also, ReFS mostly was designed for virtualization while NTFS is the better choice for the file server.

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