Here is an excerpt from "Professional Biztalk Server 2006" book explaining wich is the most appropiate identifier for a message in BizTalk:
"The most appropriate identifier to use is the BTS.InterchangeID message context property. The interchange ID is a GUID that is created by the engine. It is flowed automatically by the Messaging Engine as the message passes through the pipeline. You should note that the Message ID is typically not appropriate, since the message may be cloned multiple times during its processing, as described in Chapter 4, and each clone will have a unique Message ID. The Orchestration Engine will also flow the BTS.InterchangeID message context property where it can, although you must flow the property yourself in scenarios in which you create new messages"
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