<?xml version="1.0" encoding="ASCII"?>
<xmi:XMI xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:designmodel="http://www.example.org/designmodel">
  <designmodel:State name="Waiting"/>
</xmi:XMI>

<?xml version="1.0" encoding="ASCII"?>
<xmi:XMI xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:designmodel="http://www.example.org/designmodel">
  <designmodel:State name="Ready"/>
</xmi:XMI>

      new XMIResourceImpl(resourceURI)
      {
        @Override
        protected boolean useUUIDs()
        {
          return true;
        }
      };

ResourceSet rs = new ResourceSetImpl();
rs.getResourceFactoryRegistry().getExtensionToFactoryMap().put("ecore", new XMIResourceFactoryImpl());
Resource res = rs.createResource(URI.createFileURI(PATH_TO_ECORE_FILE));
res.load(null);
EPackage metapackage = (EPackage) res.getContents().get(0);
EFactory metaFactory = metapackage.getEFactoryInstance();

   <extension point="org.eclipse.emf.ecore.extension_parser">
      <!-- @generated library -->
      <parser
            type="library"
            class="org.eclipse.example.library.util.LibraryResourceFactoryImpl"/>
   </extension>

<extension point="org.eclipse.emf.ecore.extension_parser">
      <!-- @generated designmodel -->
      <parser
            type="designmodel"
            class="mic.model_code_synchronization.designmodel.util.DesignmodelResourceFactoryImpl"/>
   </extension>

ResourceSet rs = new ResourceSetImpl();
rs.getResourceFactoryRegistry().getExtensionToFactoryMap().put("ecore", new XMIResourceFactoryImpl());
Resource res = rs.createResource(URI.createFileURI("C:/.../.../designmodel.ecore"));
res.load(null);
EPackage metapackage = (EPackage) res.getContents().get(0);
EFactory metaFactory = metapackage.getEFactoryInstance();

ResourceSet savingResSet = new ResourceSetImpl();
		savingResSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi", new XMIResourceFactoryImpl());

XMIResource savingRes = (XMIResource) savingResSet.createResource(URI.createFileURI(outputPath), null);
savingRes.getDefaultSaveOptions().put(XMIResource.OPTION_KEEP_DEFAULT_CONTENT, Boolean.TRUE);
//adding the created EObjects to this savingRes...
savingRes.save(Collections.EMPTY_MAP);
//this returns null
saving.getID(someEObject_I_created);

rs.getResourceFactoryRegistry().getExtensionToFactoryMap().put("ecore", new DesignmodelResourceFactoryImpl());

//method getting called with the user-modified instance
public void updateDataRepresentation(Resource updatedModel) {
		updatedModel.getContents().forEach(updatedModelElement -> {
			
			//getting respective model element in existing designmodel (existentDesignmodel is simply a Resource of the previously saved version of the instance)
			EObject existentModelElement = existentDesignmodel.getEObject(updatedModel.getID(updatedModelElement));
			
			if(existentModelElement == null) {
			//no existend model element there yet, meaning it got added by the user through modifications at the design model
				System.out.println(updatedModelElement + " was newly created");
				//TODO create data object
				return;
			}
			
			//MappingEntry is a data object consisting of the EObject and its respective data object it gets mapped to (+ some other stuff)
			//see below for these helper-methods
			MappingEntry entry = getMappingEntryByModelelement(existentModelElement);
			if(entry == null) {
				entry = getMappingEntryByID(updatedModel.getID(updatedModelElement));
			}
			//this is where I change the internal date object according to the (maybe updated) new model element
			entry = updateMappingEntry(entry, updatedModelElement);
		});
		
		[...] //here I also go through the existentDesignmodel-contents to check if it contains an element that got removed in the updatedModel to then delete it in the respective data objects I maintain
		
		//setting the existent model to the newly updated one after modifying the data objects in my code
		this.existentDesignmodel = updatedModel;
	}
	//helper methods from above
	private MappingEntry getMappingEntryByModelelement(EObject modelelement) {
		for(MappingEntry e: this.mappings) {
			if(e.getDesignmodelElement().equals(modelelement))
				return e;
		}
		return null;
	}
	
	private MappingEntry getMappingEntryByID(String id) {
		for(MappingEntry e: this.mappings) {
			EObject o = e.getDesignmodelElement();
			String existentID = this.existentDesignmodel.getID(o);
			if(existentID.contentEquals(id))
				return e;
		}
		return null;
	}

<designmodel:State xmi:id="cb33c7a3-8769-479e-bbc3-f4b36363b658" name="Ready"/>
<designmodel:State xmi:id="f9ad4afa-1d4f-46cf-982d-d49cdbaf8a90" name="Waiting"/>

<?xml version="1.0" encoding="ASCII"?>
<xmi:XMI xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:designmodel="http://www.example.org/designmodel">
  <designmodel:State xmi:id="0f359d4a-5154-462c-90aa-e125197cdb6d" name="Ready">
    <transition href="#7880aa8f-1e86-42e0-a212-e91326292d31"/>
  </designmodel:State>
  <designmodel:Transition xmi:id="7880aa8f-1e86-42e0-a212-e91326292d31" name="switchToWaiting"/>
</xmi:XMI>

<?xml version="1.0" encoding="ASCII"?>
<xmi:XMI xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:designmodel="http://www.example.org/designmodel">
  <designmodel:State xmi:id="0f359d4a-5154-462c-90aa-e125197cdb6d" name="Ready">
    <transition href="#7880aa8f-1e86-42e0-a212-e91326292d31"/>
    <transition href="#11111111-2222-3333-4444-ffffffffffff"/>
  </designmodel:State>
  <designmodel:Transition xmi:id="7880aa8f-1e86-42e0-a212-e91326292d31" name="switchToWaiting"/>
  <designmodel:Transition xmi:id="11111111-2222-3333-4444-ffffffffffff" name="userAddedTransition"/>
</xmi:XMI>

//get target-class of the containment reference
EReference classReference = (EReference) holdingClass.getEStructuralFeature(referenceName);

String targetClassName = classReference.getEReferenceType().getName();
EClass targetClass = (EClass) metapackage.getEClassifier(targetClassName);

//create contained model element object
EFactory metafactory = metapackage.getEFactoryInstance();
EObject targetInstance = metafactory.create(targetClass);

//parentObject in this case would be the State-instance, so I first get the existing contents to then add the new reference to it
List<EObject> refs = new ArrayList<>(parentObject.eContents());
refs.add(targetInstance);
parentObject.eSet(classReference, refs);

<?xml version="1.0" encoding="UTF-8"?>
<ecore:EPackage xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:ecore="http://www.eclipse.org/emf/2002/Ecore" name="designmodel" nsURI="http://www.example.org/designmodel" nsPrefix="designmodel">
  <eClassifiers xsi:type="ecore:EClass" name="State">
    <eStructuralFeatures xsi:type="ecore:EAttribute" name="name" eType="ecore:EDataType http://www.eclipse.org/emf/2003/XMLType#//String"
        iD="true"/>
    <eStructuralFeatures xsi:type="ecore:EReference" name="transition" upperBound="-1"
        eType="#//Transition" containment="true"/>
  </eClassifiers>
  <eClassifiers xsi:type="ecore:EClass" name="Transition">
    <eStructuralFeatures xsi:type="ecore:EAttribute" name="name" eType="ecore:EDataType http://www.eclipse.org/emf/2003/XMLType#//String"
        iD="true"/>
  </eClassifiers>
</ecore:EPackage>

//loading in the updated model via a helper method as an XMIResource
XMIResource updatedModel = Utility.loadExistingModel(existingModelPath);	

//iterating over the objects directly contained in the resource (so all State- and Transition-objects get reached here, since they are root objects themselves)
updatedModel.getContents().forEach(updatedModelElement -> {
	System.out.println(updatedModelelement + updatedModelElement.eContainer());
});