Mex,
What you could try is a project transfer to a local eap file, import export there to to duplicate the folder structure, and then transfer the project back to Oracle.
This means however that you can't work on the oracle model why you are doing this, as the project transfer will destroy the Oracle repository.
Another option is to automate the export/import of each package individually.
The Project Interface contains operations
ExportPackageXMI (string PackageGUID, enumXMIType XMIType, long DiagramXML, long DiagramImage, long FormatXML, long UseDTD, string FileName)
and
ImportPackageXMI (string PackageGUID, string Filename, long ImportDiagrams, long StripGUID)
So calling those in the correct order should result in the required duplicate.
Geert