your problem would be clearer if you provided a sample input and the
result you want. I think your smple input is really just an incomplete
descriptiuon, not something to pass as input to a stylesheet?

Input:
=======

 <affil>
 [1] 1This is the first affiliation (which repeats), will appear once in
affiliation list
 [2] 2This is the second affiliation, University of Wisconsin-Madison,
Madison, WI, USA</affil>




what repeats? If it repeats does do all the repeats  get the sma enumber
in brackets and/or the same number after the bracket.
If you remove duplicates do teh remaining ones have to be renumbered,
....

David

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