There is no existing code to do this. You would have to write an Eclipse headless application that does something like this:
IPreferencesService service = Platform.getPreferencesService();
IExportedPreferences prefs = service.readPreferences(file input stream);
// TODO create IPreferenceFilter array to filter what you want
service.applyPreferences(prefs, filter array);
See the source of the import preferences page org.eclipse.ui.internal.wizards.preferences.WizardPreferencesImportPage1
for an example.