So, if you read through the link that @PhilipDAth posted, the answer was in there, but slightly hidden
To remove an app from the VPP list in Systems Manager involves you going to either school.apple.com or business.apple.com (whichever is appropriate)
Click Apps and Books on the left hand side, then find the appropriate app,
Find your MDM server (there may be only one) and transfer the licenses either back to, in the case below, your ASM / ABM instance, or to another MDM server:
and
In the case above, Cisco Meraki + MDM Developer is the name of my ASM instance, and is NOT an MDM server. You can use this as a parking lot / dumping ground