Storage Utilization

i think Windows does not directly wipe the deleted files "either from dedupe or other deletion" so the storage layer will always see used blocks of these deleted files.
i do not know about AHV, but i think you have to zero-fill the deleted blocks using sdelete or other tools to let the storage layer know these blocks are not used anymore so it can reclaim its used space.

So Nutanix will leverage capacity dedupe on new writes, not existing extents. One trick is to use a tool called vdisk manipulater for fingerprinting existing data. This will make the storage think it's a new write and will dedupe it. I'd recommend talking to support. They will gladly assist.

This link talks about the fingerprinting process.

https://portal.nutanix.com/#/page/docs/details?targetId=Advanced-Admin-AOS-v59:sto-vdisk-manipulator-t.html

Another alternative is to create a new container with capacity dedupe and migrate the VM to the new container. Keeping your overall capacity in mind. Both will generate additional I/O I've done both and it helps.