You can maintain the application component hierarchy in RSA6. There are options to create/delete/rename and move hierarchy nodes under the Hierarchy menu.
To transport a modified version of the RSA6 application component hierarchy you will have to manually add it to a transport by adding R3TR DSAA APCO (to transport the inactive version of the hierachy use R3TR DSAD APCO).
If the application hierarchy is in the $TMP package you first have to set it to a transportable package as follows:
If your application component hierarchy is assigned to local object then first you need to change the package.
Go to TCode: SE03
For Object Type Selection use: DSAA
Now change object directory from $TMP to the one being used in your project.
See SAP note 382471 – BW-OLTP-APCO: How do I transport it?
Also check OSS note 542454
See also: http://scn.sap.com/thread/228915
Technique for switching ECC source systems in SAP BW Environment without affecting the
data modeling objects in the BW environment. By data modeling objects, we mean transformations, update rules and transfer rules getting inactive or getting deleted. Once the source system is switched, data reload needs to happen to have the initializations and deltas to come from the new source system. Also we have to ensure that the data from old source system( both transactional and master ) needs to be deleted in the BW system before reloading from the data from new source system to ensure consistency in the data from new system.
The following SCN Article describes the procedure
Step by Step on Changing ECC Source Systems without Affecting Data Modeling Objects in SAP BW
See also 110849 – “Error during insert in port table” (create source system) if the error occurs during the RSA1 / Source System / Restore step