I used PDQ Deploy to create a batch file calling wmic to uninstall the agent on machines that were not reporting in see below for command.
wmic product where name="ESET Management Agent" call uninstall
This removed the agent from all machines that were stuck in between on-premise and cloud,
I then deployed the agent also using PDQ Deploy ( Used the 7 day free trial although I am planning on purchasing now as its a very useful tool)
Hopefully this helps someone else who is also having issues with migrating.
Lightmeup1 received kudos from jimwillsher in Migrating from on-prem to cloud Protect issues