I have never heard of such a method of citation, and endnote depends on the sort order in the bibliography to define the numbering system, not the citation. So while, in endnote, you have options to sort citations in a order different from that in the bibliography, that parameter is applied to how a group of citations used at once in the text, are ordered (1-3). The bibliography sort order (by appearance or by alpha) is going to define now they are numbered, so what you are seeing, is not a surprise.
Without tedious manual manipulation of a custom field in each of the records in your database (which could not be easily automated), I don’t see an easy way around this.
Where is this output style required in a dissertation? Are you sure you are interpreting the instructions correctly?