For upgrading to EHP4 we have added parameter SAPLOCALHOST to change hostname from upper to lowercase. Thies lead to some issues, which are solved now. However, the Solution Manager is no longer able to show alerts in System Monitoring. I have re-registered the CCMS agents, checked all RFC's, all data in SMSY but no luck. In SMSY I found the instances in uppercase (with an inactive mark next to it), but deletion of these had no effect. In the System Component Repository (RZ21), the system shows up with both upper and lowercase caracters. The uppercase one has no data under it, so I am afraid this is the one that's used. It looks like new data is added, but old data isn't removed.
Is there a way to manually delete these systems from the SCR?