There should be two check-in boxes (a damaged issue box and a suppressed perfect copy box). Upon seeing these two boxes you will know that you have received the replacement copy. Examine the replacement to make sure it's in good condition and/or make any necessary repairs or consultations w/ binding.
To check in the perfect copy:
Obtain the damaged copy from claims agent’s shelf and:
Occasionally, when a free replacement of a journal is unavailable or an issue of a journal is lost, the Preservation, Conservation, and Teaching Coordinator might make a decision to have the Serials Acquisitions Manager purchase a replacement copy. The Serials Receiving Specialist assists with the handling of these items, for example, with labeling.