I have an idea off the top of my head think it should work. Here it is..before u start processing the batch create a new message, that contains this unique id by calling a sequence in the oracle database, this should be just like executing any other statement on the db.
Now put this sequence output message field in one of the fields in each message of the child records, in a construct message. Since the orchesration is executed newly for each file this should work..what say? Let me know
What you could optionally do is call a stored procedure and pass the entire xml,. although this would not be the "biztalk" way of doing things.
-Mahesh