EXMerge is your friend

Each item in your mailbox is defined by a set of MAPI properties (PR_SOMETHING_OR_OTHER). The size of a message is a particular property (PR_MESSAGE_SIZE). So is the delivery date, when it was last modified, and even the text of the message (PR_BODY). There are also properties that are for uniquely identifying the message and comparing two messages to see if they are the "same." PR_SEARCH_KEY can be used to find correlated messages, and then you can do additional property comparisons to determine whether they are the same message (however you are defining "same" for your purposes). EXMerge not only determines if two messages are the same, but checks for later versions of the same message, and will replace an older version with an updated version as appropriate.