Encontrou a resposta no wiki do Arch!
O comando específico foi VBoxManage closemedium disk VMShare/external.vmdk
Código completo:
# remove old vmdk
echo "Removing old"
eval "VBoxManage storageattach Windows --storagectl "SATA" --port 1 --device 0 --type hdd --medium none"
eval "VBoxManage closemedium disk VMShare/external.vmdk"
eval "rm VMShare/external.vmdk"
# create new vmdk and add it
echo "Creating new"
eval "VBoxManage internalcommands createrawvmdk -filename VMShare/external.vmdk -rawdisk /dev/$part"
eval "VBoxManage storageattach Windows --storagectl "SATA" --port 1 --device 0 --type hdd --medium VMShare/external.vmdk"