Resolution:
Unfortunately, the messages in the ledger file cannot be removed selectively even though you know what messages can be removed directly by manipulating the ledger file.  You could modify the example program cmlistener.java under TIBCO_HOME/src/examples/java to listen and confirm all the messages on the subject using the same CMNAME.  When you run this, all the messages will get confirmed and removed and the ledger file will eventually shrink in size.  But if you republish the message, the message will goto the publisher's ledger file one more time as a new message (it has a new seq num), the original message will not be removed.