replace-advice.el

(defvar *replace-count-base* 0)
(defvar *replace-count-format* "%d")

(defadvice query-replace-compile-replacement
  (after replace-count-format)
  "Change \\# format of (query-)replace-regexp"
  (when (consp ad-return-value)
    (let ((oldexp '(number-to-string replace-count))
          (newexp '(format *replace-count-format*
                           (+ replace-count *replace-count-base*) )))
      (if (and (eq (car ad-return-value) 'replace-eval-replacement)
               (equal (cdr ad-return-value) oldexp) )
          (setcdr ad-return-value newexp) ; only \#
        (let ((lst ad-return-value))
          (while lst
            (if (equal (car lst) oldexp) (setcar lst newexp))
            (pop lst) )) ))))

(ad-activate 'query-replace-compile-replacement)