It depends on the VDP version.
If you are running 5.5 - You can re-deploy a new VDP appliance but you can still point the de-dupe disks from the old appliance (From disk-1 on-wards).This way you are not loosing the previous backups. You just need to power-off the old appliance.
If you are running below 5.5 version - You do not have an option other than to re-deploy the appliance. Just power-off the appliance and delete it. Even if you see the VDP plug-in in the UI, you do not really have to care about it. Re-deploy a new appliance as usual.