The windows installer is broken

That is done by design. As long as the VMs have already been imported there will be not adverse affects: See Deleting a whonix ova file

I believe the installer does this to free up disk space and if you want to install an updated whonix.ova disk image in the future the older one will not be confused with the newer one. Thats what I remember from when I user Vbox anyways.

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