If you installed VirtualBox and later changed your mind to use the .vdi file with kvm, it will work, but when you go back to VirtualBox, it cannot be used.
This is because, when it was opened with qemu/kvm, the owner and group became root.
To open the file again in VirtualBox, open a terminal window and enter the following:
sudo chown user.group *.vdi
where user is your userid and the group is your primary group.
Now it will work with VirtualBox again.