A little confusing.. Is the end result a VM only setup? If it is, 2007 can not be used on the same server.
If it's VM only, 2003 onbox is only allowed with Unity 5/7.
For migrating or upgrading, it all depends. Most likely they have Windows 2000 running with 4.05. An OS re-install is required. Which entails either a new server with Windows 2003 and 4.05 running (Dirt backup, Dirt restore) or a new server running Unity 7.x and use Cobras to migrate.
The licenses in 4.x really did not matter if they were purchased as UM or VM. Unity does not know whether or not your Exchange is Production (email) or is a stand alone Exchange "Message Store" for Unity. The Class of Service does restrict UM features, but it will still work as a stripped down UM model. All depends how you classify UM these days.
With VM Mode, techically from Cisco view, the voicemail should never end up in the subscribers email box. This would UM and should have a UM license. If the partner set it up to do this with a VM license, technically, it's not support and could be a violation. A simple upgrade of the VM to UM license is needed to cover this then.
So basically, you will need first sort out what licenses they actually have. If they have VM only license, they will need to purchase the upgrade license from VM to UM. Its like 15-20 a pop I think. Or have Cisco change them to CUWL licensing.
Once you have the licensing figured out, do you have a new server or reusing the old server?
I would recommend a new server. Get it loaded up with Unity 7.x, then use the GSM tool to migrate the Subscribers over, then use Cobras to migrate the CallHandlers. You will need to rebuild the System settings, COS, templates, etc though.
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