" provisioned and managed" device only means that you are done with that device and all is ok for now. But, if you want to change something, you need apply a new tamplate and provision again. That´s how things works.
"Please correct if I am wrong, when we provision the device DNAC will only push changes that were made not full config ?"
There are two way to change device configuration. By using template, which is very similar to access the device using CLI, the different is that the DNAC will do this for you and apply those commnad that you put on the tamplate. This can be done for one device or all device and you´ll be changing only the configuration you added on the template.
You can also go to "Provision"> "Fabric">Device
There you can change configuration in one device at a time. In your case, as you want to delete VNs, it may be better do this way.
On the device, go to "Host Onboarding" and "Virtual Networks". You are going to see your VNs. You can delete or add or change and this will happen to only this device.