How are papers containing security markings like “Secret” or “Confidential” treated by the USPTO?

The MPEP states:

All applications or papers, including non-patent literature, in the U.S. Patent and Trademark Office bearing words such as “Secret,” “Confidential,” “ITAR” or similar must be promptly referred to Licensing and Review for clarification or security treatment.

These papers cannot be placed in public records like patented files until the security markings are declassified or explained.