How to respond to "the reference sign does not appear in the drawings" in the patent examination opinion so that the modification does not exceed the scope?

The simplest way is to delete the reference signs (such as 125) that do not appear in the drawings from the description (for example, change all "element 125" in the description to "element" ). This won't go out of scope. Of course, it is best to communicate with the examiner over the phone to modify the method before submitting your response, just in case.