Resolution:
TIBCO Runtime Agent (TRA) document specifies the following procedure for changing the database for a domain:

Domain Utility User's Guide -> Chapter 3 Server Settings and Migration -> Changing the Database for a Domain

To Change the Database Using the GUI

1. Start Domain Utility on the machine on which the administration server for the domain is running and click the Next button on the main screen.
2. Under Category, click Server Settings, then click Database Configuration.
3. Click Next and in the screen that appears, select the administration domain to change.
4. In the next screen change the values for your database connection. Click the Test Connection button to verify the values. See Database Connection Fields for details.
5. Click Next to review the values you supplied.
6. Click Next to apply the values.
7. Click Finish to end the session.
8. Manually update the database URL by executing the following SQL statements.

update AdMap set value = 'New_DB_URL' where mapkey = 'tibcoadmin.database.url' and value = 'Old_DB_URL'

update App_Domain_PrefixMap set value = 'New_DB_URL' where mapkey = 'tibcoadmin.database.url' and value = 'Old_DB_URL'

9. Restart the TIBCO Administrator administration server.
---------------------------------------------------------------

Regarding the SQL statement
--------------------------------
You need to replace the "App_Domain_Prefix" with specific Table Prefix of specific application domains.
To get the "App_Domain_Prefix", please go to the Admin GUI, click Resource Management > Applications Domains, click the application domain, the Table Prefix  in tab General shows the "App_Domain_Prefix" value.  (It could be PA,PB, PC,PD,  etc.)

In summary, there is no table App_Domain_PrefixMap, but <App_Domain_Prefix>Map. You need to update
      - AdMap
      - AuMap
      - PaMap
      - PbMap
      - And other table <App_Domain_Prefix>Map, if you have more application domains.
--------------------------------

Go through the steps above to make sure the procedure is correct. Also be sure to restart the Admin server after the changes.

NOTE: 

• This solution is relevant for TRA 5.6.0 and previous version of TRA ,with TRA 5.7.0 onwards you no more have to make any manual modification to database MAP tables listed in step 8 above.
• Before making any modifications please make sure you take a back of your DB tables.

[SME Approved]TIBCO Administrator tries to connect to an old databaseURL afterchanging the DB parameters in the Domain utility.