If you are wondering where the individuals that were previously in geo.owl have gone, they have been moved to other OWL files according to a modularization strategy that seeks to avoid compiling all possible geographical entities into one, giant, outsized file.
For example: nations and their dependencies are now in nation-and-dependency-instances.owl available at http://purl.obolibrary.org/obo/geo/nation-and-dependency-instances.owl
For a full list of PURLs, see the geo.yml file here: https://raw.githubusercontent.com/OBOFoundry/purl.obolibrary.org/master/config/geo.yml
When citing the Geographical Entities Ontology (GEO), use the permanent URL of the ontology: http://purl.obolibrary.org/obo/geo.owl. When referencing a specific component of GEO such as a class, object property, or individual, use that component's Uniform Resource Identifier (URI).