Messages are identified in two ways:
"id", their message ID, in the source code called just id (as opposed to message_id), which is the message's "Message-ID" field value if usable (i.e. there is exactly one such header, and it has some non-empty content), or a newly created ID to take its place. Meant to identify a particular post. Newly created IDs are currently using the identify string as described below. See better_Id_generation for suggestions to change this.
"identify" string: identification of the mailbox and the index of the message therein. Can be used to find the original message unambiguously, see the ml2json --deidentify option. In cases where the same post appears multiple times in the same or different mailboxes, there will be multiple "identify" values, but only one and the same "id" value; a warning will be issued if that happens and all except one instance of the post will be ignored.
identify = md5(path_to_the_mailbox) + "/" + position_within_the_mailbox
or whatever else the mailbox_path_hash config option is set to.
Note that path_to_the_mailbox is not expanded (made absolute), but directly derived from the source path given to ml2json. See better_Id_generation for suggestions to change this.