This comment was written a while ago, so I can't recall exactly what my thought process was. The relation instances caches the schema instances of the parent schema and the current target schema. The parent schema instances are preserved in the form of attributes and relation instances of its child (the current target schema). And since the target schema is to be discarded, its instances need to not be preserved (as per your comment below). Because of this reasoning, I believe the relation instances can be safely discarded.

This is different from ontologylink schemas since their schema instances contain actual string values that will not be preserved if the instances are discarded. The non-ontologylink schemas are more like a container of their child attributes and schemas, with no extra information to preserve.