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What I have done in the past, and seems to work, is execute an Interface or Procedure in simulate mode, choosing the agent that you would like to use in reverse engineering the XML. Then, attempt to reverse engineer the file again. Not sure if this will work, but it has for me at times. You might also try this and restarting ODI to clear out anything 'cached' in the JVM.
It seems ODI is caching the agent that you are using - but I'm not sure how to properly change it.