After the IF13 installation, the MySAP agent always discovers a SAP instance subnode that no longer exists on SAP (see also http://www-01.ibm.com/support/docview.wss?uid=swg21515555).
By following the instructions in technote 1515555: http://www-01.ibm.com/support/docview.wss?uid=swg21515555
the unwanted instance is no longer registered to ITM, so it does not appear on TEP.
Anyway, the ITM ABAP module /IBMMON/ITM_HOSTS is still able to find the old instance and to perform some actions leading to error messages being recorded into the SAP System Log.
Resolving the problem
The error messages are of course harmless because related to an old, inactive SAP instance.
Anyway, if you want them to be no longer recorded, you need to completely remove the instance definition from the monitored SAP system.
The ITM ABAP code tries to retrieve SAP instance information also from the SAP table TPFID.
So, if the unwanted instance is not showing neither from the RZ04 TCode nor in the output of the TH_SERVER_LIST function module, and you already followed the steps suggested by technote
http://www-01.ibm.com/support/docview.wss?uid=swg21515555 then check the content of table TPFID using TCODE SE16.
If the old instance is still defined in there, ask the SAP administrator to delete the entry from this table.
Once removed, the ITM ABAP code will no longer discover the old instance and the error messages will not be logged into the SAP System Log.
IBM Tivoli Monitoring mySAP Agent V6.2