Quick question - is it possible that the entity (or entities) in question are defined in an external DTD that is referenced by your SGML documents? If so, I don't think the entities would be embedded in the document as they are in the external DTD. What you've shown looks like an internal DTD subset.
If you want these entities embedded for use by external tools or downstream consumers than they should use an SGML parser for these documents. The SGML parser will read the associated DTD so the full set of entities are available.
