Trying to understand why libgdx wipes existing models when creating new ones

Question

I'm coding a simulated brain and I'd like to make an arrow appear when one cell connects to another cell.

My output without generating an arrow looks like this:

Where each block rendered represents a cell in a 8x8x1 grid.

The cells are programmed to seek out another cell when they haven't had a pulse in a hundred ticks. When they find another cell I'd like to draw an arrow between them to visualize the link. This arrow is created in my method onAxonConnected()

But at my first attempt to make the arrow as the connection is established it seems to completely wipe the rendering of the existing cell blocks. I've had no issues in creating new cell blocks when a new cell was grown dynamically, so why this gives problems mystifies me.

As you can see in the below image there is one well defined arrow and what seems to be a lot of stretched out lines that may or may not be the cell blocks.

This is my very first time experimenting with libgdx and i'm eager to learn more about it, but except for LibGDX creating ModelInstance after create() has ended without an answer I haven't found anything that comes close to my scenario.

My Question

What causes the cell blocks to not render when arrows are introduced?

Below is the code I'm using for the rendering.

public class MyGdxGame implements ApplicationListener, IBrainEventListener {

 @Override
 public void onAxonConnected(Pos one, Pos two) {

  Model lineModel = build.createArrow(one.x, one.y, one.z, two.x, two.y, two.z, 0.15 f, 0.05 f, 5, GL20.GL_TRIANGLES, new Material(), VertexAttributes.Usage.Position | VertexAttributes.Usage.Normal);
  ModelInstance line = new ModelInstance(lineModel);
  this.addArrowModelInstanceToRender(line);
 }


 protected void addModelInstanceToRender(ModelInstance render) {
  ArrayList < ModelInstance > newlist = new ArrayList < ModelInstance > (this.modelRenders.size() + 1);
  newlist.addAll(this.modelRenders);
  newlist.add(render);
  this.modelRenders = newlist;
 }

 protected void addArrowModelInstanceToRender(ModelInstance render) {
  ArrayList < ModelInstance > newlist = new ArrayList < ModelInstance > (this.arrowmodelRenders.size() + 1);
  newlist.addAll(this.arrowmodelRenders);
  newlist.add(render);
  this.arrowmodelRenders = newlist;
 }

 @Override
 public synchronized void onCellGrown(Cell cell, Pos pos) {

  ModelInstance render = new ModelInstance(model);
  render.transform.setToTranslation(pos.x, pos.y, pos.z);
  this.addModelInstanceToRender(render);


  ArrayList < CellRender > newCellRenders = new ArrayList < CellRender > (cellRenders.size() + 1);
  newCellRenders.addAll(cellRenders);
  CellRender renderManager = new CellRender(cell, render);
  newCellRenders.add(renderManager);
  cell.setPulseListener(renderManager);

  this.cellRenders = newCellRenders;

 }

 @Override
 public synchronized void onAxonFired(Cell cell, Axon axon, Pos pos) {

 }


 PerspectiveCamera cam;
 CameraInputController camMove;
 ModelBatch batch;
 Model model;
 ModelBuilder build;
 ModelInstance renderer;
 ArrayList < ModelInstance > modelRenders;
 ArrayList < ModelInstance > arrowmodelRenders;
 Environment enviroment;
 ArrayList < CellRender > cellRenders;

 BrainBoot brainBooter;
 Brain brain;

 Texture texture;
 SpriteBatch spriteBatch;

 @Override
 public void create() {

  modelRenders = new ArrayList < ModelInstance > ();
  arrowmodelRenders = new ArrayList < ModelInstance > ();
  cellRenders = new ArrayList < CellRender > ();
  texture = new Texture(Gdx.files.internal("android.jpg"));
  spriteBatch = new SpriteBatch();
  brainBooter = new BrainBoot();
  brain = brainBooter.getBrain();

  cam = new PerspectiveCamera(50, Gdx.graphics.getWidth(), Gdx.graphics.getHeight());
  cam.position.set(16 f, 8 f, 16 f);
  cam.lookAt(8 f, 8 f, 8 f);

  cam.near = 1 f;
  cam.far = 300 f;
  cam.update();

  enviroment = new Environment();
  enviroment.set(new ColorAttribute(ColorAttribute.AmbientLight, 0.4 f, 0.4 f, 0.4 f, 1 f));
  enviroment.add(new DirectionalLight().set(0.8 f, 0.8 f, 0.8 f, -1 f, -0.8 f, -0.2 f));

  batch = new ModelBatch();
  build = new ModelBuilder();

  model = build.createBox(0.5 f, 0.5 f, 0.5 f,
   new Material(ColorAttribute.createDiffuse(Color.PURPLE)),
   VertexAttributes.Usage.Position | VertexAttributes.Usage.Normal);

  brain.addEventListener(this);

  camMove = new CameraInputController(cam);

  Gdx.input.setInputProcessor(camMove);

  brainBooter.boot();
 }

 @Override
 public void render() {
  ArrayList < CellRender > cellRenderList = this.cellRenders;
  for (CellRender r: cellRenderList) {
   if (r.dirty) {
    r.clean();
   }
  }
  Gdx.gl.glClearColor(1, 1, 1, 1);
  Gdx.gl.glClear(GL20.GL_COLOR_BUFFER_BIT | GL20.GL_DEPTH_BUFFER_BIT);
  camMove.update();

  ArrayList < ModelInstance > renderers = modelRenders;
  ArrayList < ModelInstance > arenderers = arrowmodelRenders;

  batch.begin(cam);

  batch.render(arenderers, enviroment);
  batch.render(renderers, enviroment);


  batch.end();

 }

 @Override
 public void dispose() {
  batch.dispose();
  model.dispose();
 }

 @Override
 public void resize(int width, int height) {}

 @Override
 public void pause() {}

 @Override
 public void resume() {}
}

Answer 1

The problem was caused by giving the command to create the arrow from an event that was triggered from a separate running thread.

This separate running thread was the cause somehow that everything went awry when it fired off an event that instantiated the model and added it to the arraylist for the next rendering cycle.

When I put the separate thread in line with the main render thread I was able to instantiate new arrows without issue.

Lesson learned: don't use threads with Libgdx and if you do, use PostMessages.