I was unable to remove the agent from the affected system. Removing all products and the agent via epo did not actually remove the agent (rebooting mulitple times) and the removal tool did not work because it's an enterprise product.
I'm now in contact with support.
- remove everything using enterprise removal tool
- delete mcafee related keys at HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Installer\Products (without this step I was not able to reinstall agent and extensions)
- reinstall agent and extensions via epo and run update
system is up to date and does not show up as duplicate anymore
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