It depends.
If I was making a single server that was important, I would certainly create as many virtual disks as necessary. For instance at work our servers have an OS VHD and a Data VHD - and our database servers have extra on top of that. So if one breaks or needs to be migrated, we can just...
So to clarify: you use rsync -av to copy the files (not move), ensure it's all there, then format the drive (ext4 is fine) and then copy them back.
Moving using GUI is also an option. But moving isn't strictly necessary since you're going to be wiping the drive anyway. It's just doing an extra...
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