Program: 160653
Project: 160653
Buggy source:
@SuppressWarnings({"String_Node_Str","String_Node_Str"}) private void fixExplicitNullReferences(){
  for (  IdEObject idEObject : newModel.getValues()) {
    if (idEObject instanceof IfcRoot) {
      String guid=((IfcRoot)idEObject).getGlobalId().getWrappedValue();
      for (      EReference eReference : idEObject.eClass().getEAllReferences()) {
        if (eReference.isMany()) {
          List list=(List)idEObject.eGet(eReference);
          List oldList=(List)resultModel.get(guid).eGet(eReference);
          Set<Object> guidsToRemove=new HashSet<Object>();
          for (          Object o : oldList) {
            if (o instanceof IfcRoot) {
              String referredGuid=((IfcRoot)o).getGlobalId().getWrappedValue();
              if (newModel.contains(referredGuid)) {
                boolean found=false;
                for (                Object q : list) {
                  if (q instanceof IfcRoot) {
                    String qGuid=((IfcRoot)q).getGlobalId().getWrappedValue();
                    if (qGuid.equals(referredGuid)) {
                      found=true;
                      break;
                    }
                  }
                }
                if (!found) {
                  guidsToRemove.add(referredGuid);
                }
              }
            }
          }
          if (!guidsToRemove.isEmpty()) {
            LOGGER.info("String_Node_Str");
            oldList.removeAll(guidsToRemove);
          }
        }
 else {
          if (idEObject.eGet(eReference) == null) {
            Object eGet=resultModel.get(guid).eGet(eReference);
            if (eGet != null) {
              if (eGet instanceof IfcRoot) {
                String oldGuid=((IfcRoot)eGet).getGlobalId().getWrappedValue();
                if (newModel.contains(oldGuid)) {
                  LOGGER.info("String_Node_Str");
                  resultModel.get(guid).eSet(eReference,null);
                }
              }
            }
          }
        }
      }
    }
  }
}

Fixed version (ground truth):
@SuppressWarnings({"String_Node_Str","String_Node_Str"}) private void fixExplicitNullReferences(){
  for (  IdEObject idEObject : newModel.getValues()) {
    if (idEObject instanceof IfcRoot) {
      String guid=((IfcRoot)idEObject).getGlobalId().getWrappedValue();
      for (      EReference eReference : idEObject.eClass().getEAllReferences()) {
        if (eReference.isMany()) {
          List list=(List)idEObject.eGet(eReference);
          List oldList=(List)resultModel.get(guid).eGet(eReference);
          Set<Object> guidsToRemove=new HashSet<Object>();
          for (          Object o : oldList) {
            if (o instanceof IfcRoot) {
              String referredGuid=((IfcRoot)o).getGlobalId().getWrappedValue();
              if (newModel.contains(referredGuid)) {
                boolean found=false;
                for (                Object q : list) {
                  if (q instanceof IfcRoot) {
                    String qGuid=((IfcRoot)q).getGlobalId().getWrappedValue();
                    if (qGuid.equals(referredGuid)) {
                      found=true;
                      break;
                    }
                  }
                }
                if (!found) {
                  guidsToRemove.add(referredGuid);
                }
              }
            }
          }
          if (!guidsToRemove.isEmpty()) {
            oldList.removeAll(guidsToRemove);
          }
        }
 else {
          if (idEObject.eGet(eReference) == null) {
            Object eGet=resultModel.get(guid).eGet(eReference);
            if (eGet != null) {
              if (eGet instanceof IfcRoot) {
                String oldGuid=((IfcRoot)eGet).getGlobalId().getWrappedValue();
                if (newModel.contains(oldGuid)) {
                  resultModel.get(guid).eSet(eReference,null);
                }
              }
            }
          }
        }
      }
    }
  }
}