Resolution:
Lets us divide upgrade process into two sides. You can do the server side first followed by the client.

1). Server Side - During the server upgrade, do not create a new BusinessWorks ProcessMonitor (BWPM) database unless you want to drop all existing BWPM information. Note that old data will not be touched.  A good starting point is TIBCO BusinessWorks(TM) Process Monitor Server Release Notes->Installation->upgrade section'.  If you want to run old historic track information for old data then you need to run the optional migration script.

2) Client Side- You need to replace the bwpm.jar file where TIBCO ActiveMatrix BusinessWorks (BW) is installed. You do not need any configuration to be taken as backup. BWPM stores all client side configurations in a file located in the ‘resource’ folder of the BW application (see page 47 of the TIBCO BusinessWorks Process Monitor Client for BW User Guide). In order to pre-configure the BWPM Client using the application XML configuration file, the filename must be of the pattern: <ENGINE_NAME>_njams_config.xml. Note that this file is located in this directory: <TIBCO_DOMAIN_HOME>/applications/<APPLICATION_NAME>/resource

When the TIBCO ActiveMatrix BusinessWorks engine starts and the BusinessWorks ProcessMonitor Client is in its initialization phase, it will look for and read this configuration file. It will also send an acknowledgement that it knows about any configuration update of the BWPM Client.

For more details, refer to the attached (Filename: TIBCO_BusinessWorks(TM)_Process_Monitor_Client_for_BW_User_Guide.pdf  and  TIBCO_BusinessWorks(TM)_Process_Monitor_Server_Release_Notes.pdf).

How to upgrade TIBCO BusinessWorks™ ProcessMonitor (BWPM) 2.2.1 to 3.0.0?

TIBCO BusinessWorks(TM) Process Monitor Client for BW User Guide.pdf
TIBCO BusinessWorks(TM) Process Monitor Server Release Notes.pdf