If you only have a single entitlement to vCenter, and that vCenter has been deleted, you can reassign that license to a new vCenter and still be compliant. If this isn't what you're asking, please clarify where you're adding this license and if Veeam is complaining or vCenter is.
You should be able to generate a new license key from the My VMware portal, when you select downgrade and upgrade the license key back to the same version.
The Old license key would be invalid once you have the new license key generated.
We should be able to apply the license from the old appliance to the newly deployed appliance since the old is not active