Recover space from a VirtualBox disk

When you write large files in a dynamically sized VirtualBox disk, deleting them won’t help recovering the space at host level. The files will more likely still be on the filesystem, even if marked as free space.

To shrink a VirtualBox disk after removing large files, just zero out the rest of the drive, before asking VirtualBox to compact the disk:

On the guest:

dd if=/dev/zero of=junk # Will fail with disk full error
sync
rm junk

On the host:

find ~/VirtualBox\ VMs -name '*.vdi' -exec VBoxManage modifyhd --compact  {} \;

Here, I choose to compact all the disks, but you can just apply the -exec command to a single one.