Parentheses into Footnotes
Emacs Lisp, 335 bytes

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(defun p()(let(b(cpt 0)n)(goto-char 0)(while(search-forward"("()t)(setf b(point)n(number-to-string(incf cpt)))(backward-char)(forward-sexp)(backward-char)(kill-region b(point))(delete-backward-char 1)(delete-forward-char 1)(insert "&lt;sup&gt;"n"&lt;/sup&gt;")(save-excursion(end-of-buffer)(newline 2)(insert "&lt;sub&gt;"n" ")(yank)(insert"&lt;/sub&gt;")))))


More elegantly:

(defun parens ()
  (let (b(cpt 0)n)
    (goto-char 0)
    (while(search-forward"("()t)
      (setf b(point)n(number-to-string(incf cpt)))
      (backward-char)
      (forward-sexp)
      (backward-char)
      (kill-region b(point))
      (delete-backward-char 1)
      (delete-forward-char 1)
      (insert "&lt;sup&gt;"n"&lt;/sup&gt;")
      (save-excursion
       (end-of-buffer)
       (newline 2)
       (insert "&lt;sub&gt;"n" ")
       (yank)
       (insert "&lt;/sub&gt;")))))