By design you cannot delete the agent from the current branch and you cannot move an agent from a different branch. If you wish to place MA 4.5 in the current branch then simply check MA 4.5 into the current branch of the repository and it will overwrite the existing agent in the current branch.
Updates are not automatically deployed through EPO they require some sort of task (either defined in EPO or on the client machine) to deploy. In this case the agent is not sent out via an update task but rather via a deployment task. This is because all agent installs are (even if you are going from MA 4.0 patch 2 to MA 4.0 patch 3) is actually a complete reinstall of the agent.
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That is normal- seeing as the agent is a critial component of ePO so it makes sense to not allow deletion- you can upgrade/downgrade per branch but not delete- atleast that is how it has worked for me.
As for the patch, form what i gather, its not just the patch but the agent install with patch included- so it falls under install and for that you need a client task\product deployment. If it where a product hotfix and you didn't uncheck that global update setting when you checked it in then it would auto ddeploy.
Thanks for the replies. It makes sense now. Hopefully the day will come when I can answer questions in these groups rather than just ask them.