(defun my-reb-query-replace-regexp ()
  "Call `query-replace-regexp' with current regexp of RE-builder"
  (interactive)
  (reb-update-regexp)
  (let ((re (reb-target-binding reb-regexp)))
    (flet ((query-replace-read-from
            (prompt regexp-flag)
            ;; body
            re))
      (pop-to-buffer reb-target-buffer)
      (call-interactively 'query-replace-regexp))))

(define-key reb-mode-map (kbd "C-c %") 'my-reb-query-replace-regexp)