The following steps will allow you to update your VirtualBox Extension Pack in an environment with no desktop manager, GUI, etc. in other-words, a headless environment.
Software you should have installed before attempting this task
Change Directory to tmp
Get the latest Extension Pack at https://www.virtualbox.org/wiki/Downloads - as of this writing it's 6.1.2
Replace the old Extention
sudo VBoxManage extpack install --replace Oracle_VM_VirtualBox_Extension_Pack-6.1.2.vbox-extpack
Answer the license agreement when prompted.
very the following message:
Successfully installed “Oracle VM VirtualBox Extension Pack”.