In our test environment we successfully removed the Java stack from our central system following the instructions given in section 7.3 of the Stack Split Guide and the Software Provisioning Manager. When we restarted the system it appeared yellow in the SAP Management Console because Java was not running.
We would expect that, since the system no longer has Java, it should appear all green in the SAP Management Console. We monitor the SAP Management Console and would tend to review any system that is not appearing to be all green. So it is not good to be showing a false positive error.
We will continue trying all the normal things that one would to resolve this but if someone has had the exact same issue and resolved it I would love to hear from you as this will save us some time.