Dismount the drive you want to shrink

df -h
umount /dev/sdb

List all disks

fdisk -l # List disks

Install zerofree and shrink the disk

zerofree -v /dev/sdb

Shudown the host and shrink the guest file

Find HDD & get the original UUID

.\VBoxManage.exe list hdds

Convert to VDI

.\VBoxManage.exe clonehd "C:\Users\jnavarra\VirtualBox VMs\linux_mint_18_xfce\linux_mint_18_xfce_data.vmdk" "C:\Users\jnavarra\VirtualBox VMs\linux_mint_18_xfce\linux_mint_18_xfce_data.vdi" --format vdi

Shrink VDI

.\VBoxManage.exe modifymedium disk "C:\Users\jnavarra\VirtualBox VMs\linux_mint_18_xfce\linux_mint_18_xfce_data.vdi" --compact

Format to VMDK and delete VDI

.\VBoxManage.exe clonehd "C:\Users\jnavarra\VirtualBox VMs\linux_mint_18_xfce\linux_mint_18_xfce_data.vdi" "C:\Users\jnavarra\VirtualBox VMs\linux_mint_18_xfce\linux_mint_18_xfce_data.vmdk" --format vmdk
rm "C:\Users\jnavarra\VirtualBox VMs\linux_mint_18_xfce\linux_mint_18_xfce_data.vdi"

Set back UUID

.\VBoxManage.exe internalcommands sethduuid "C:\Users\jnavarra\VirtualBox VMs\linux_mint_18_xfce\linux_mint_18_xfce_data.vmdk" <original UUID here>