FYI Simon, if you update initramfs-tools and reboot you will again show
$ df -h /dev/vda1 Filesystem Size Used Avail Use% Mounted on /dev/vda1 4.0G 909M 2.9G 25%
This was due to the way the initramfs was mounting the disk by uuid directly rather than processing the symbolic link down to the actual device.
FYI Simon, if you update initramfs-tools and reboot you will again show
$ df -h /dev/vda1
Filesystem Size Used Avail Use% Mounted on
/dev/vda1 4.0G 909M 2.9G 25%
This was due to the way the initramfs was mounting the disk by uuid directly rather than processing the symbolic link down to the actual device.