I believe that there is an easier way to do this than to use the AF Transformer.
If the AF Databases belong to two different PI AF Servers and connect to different PI Data Archives, then you could just export and import the XML and define an Alias so that the name of the source PI Data Archive points to the Destination PI Data Archive (this would not work if both AF Databases are in the same environment).
If defining an Alias is not possible (let's say all servers reside on the same domain), then you could simply export and import the XML, then use PI Builder to change the name of the PI Data Archive. Another option is to simply edit the XML file substituting the "\\OLD_SERVER" for the "\\NEW_SERVER".
AF Transformer is good for hierarchy changes. For configuration changes in bulk, PI Builder is the best tool available.
Thanks a lot for your reply. Actually I have been editing the export xml already when moving AF databases from one server to another server to change the PI Data Archive server name. I was hoping that this operation can be achieved with AF Transformer as well, but looks like its this tool is just for transformation only.