VDI images should be backed up with the VBoxManage clonevdi tool in order to preserved file system integrity. I myself has made the mistake of copy pasting, and the result is a damaged system with many configuration changes, and files missing. I was able to salvage the contents of the VDI by getting an external ip and using ssh; whewww. To avoid potential backup meltdowns simply use the VBoxManage clonevdi tool:

VBoxManage clonevdi /home/user/.VirtualBox/VDI/example.vdi /media/usbdisk/example.vdi