If you only want to see the SYSB entry on the copied lpar(SYSB), the SYSA entry will need to be removed manually.
To modify the entries that are displayed in the Vantage Tree for CA Web Administrator for ACF2, the desired entry would need to be modified manually by editing the acf2_config.xml file.
The acf2_config.xml file is an ASCII file (not an EBCDIC file). The ASCII requirement is due to JAVA (which only runs in ASCII). USS (OMVS) can run code that is ASCII as well as EBCDIC. The issue is that OEDIT or using ISHELL are for EBCDIC and cannot be used to edit ASCII files. That is why an alternative is to FTP (in binary) the file to your PC, where you can edit ASCII files, and then FTP back (again in binary) to USS.
There are various utilities available (including from IBM) to allow direct editing of ASCII files from USS. The IBM tool is AOEDIT (and AOBROWSE plus others) that can handle ASCII files from within USS.
The location of the acf2_config.xml file resides in /tomcat/conf directory.
After making the desired change to the acf2_config.xml file, the TOMCAT server will need to be restarted for the change to take affect.