Delete then Add

adapters.application.js

import DS from 'ember-data';

export default DS.RESTAdapter.extend({
});

controllers.application.js

import Ember from 'ember';

export default Ember.Controller.extend({
  appName: 'Unload Investigation', 
  childIds: Ember.computed.mapBy('model.children', 'id'),
  all: Em.computed(function() { return this.store.peekAll('folder') }),
  allIds: Ember.computed.mapBy('all', 'id'),
});

models.folder.js

import Ember from 'ember';
import Model from "ember-data/model";
import attr from "ember-data/attr";
import { belongsTo, hasMany } from "ember-data/relationships";

export default Model.extend({
  children: DS.hasMany('folder', { inverse: 'parent' }),
  parent: DS.belongsTo('folder', { inverse: 'children' }),
});

routes.application.js

import Ember from 'ember';

export default Ember.Route.extend({
  data: { 
    folder: [
      {
        id: 1,
       	type: 'folder',
        children: [2,3]
      },
      {
        id: 2,
       	type: 'folder'
      },
      {
        id: 3,
       	type: 'folder'
      }
    ]
  },
                                  
  beforeModel() {
    this.store.pushPayload(this.get('data'));
    
    Ember.$.mockjax({url: '/folders', type:'GET', responseText: {
        folder: [
          {id: 1, type: "folder"},
          {id: 2, type: "folder", parent: 1},
          {id: 3, type: "folder", parent: 1}
        ]
    	}
    });
    
    let parent = this.store.peekRecord('folder', 1);
    for (let child of parent.get('children').toArray()) {
        this.store.unloadRecord(child);
    }
    
		this.store.query('folder', {})  
  },
  
  model() {
    return this.store.peekRecord('folder', 1);
  }
});

templates.application.hbs

<h3>UnloadRecord duplication issue</h3>
model id: {{model.id}}
<br>
all: {{allIds}}
<br>
child ids: {{childIds}}
<br>
should have 2 children but has: {{model.children.length}}
{{outlet}}
<br>
<br>

twiddle.json

{
  "version": "0.11.0",
  "EmberENV": {
    "FEATURES": {}
  },
  "options": {
    "use_pods": false,
    "enable-testing": false
  },
  "dependencies": {
    "jquery": "https://cdnjs.cloudflare.com/ajax/libs/jquery/1.11.3/jquery.js",
    "mockjax": "https://cdnjs.cloudflare.com/ajax/libs/jquery-mockjax/1.6.2/jquery.mockjax.js",
    "ember": "2.10.2",
    "ember-data": "2.11.0",
    "ember-template-compiler": "2.10.2",
    "ember-testing": "2.10.2"
  },
  "addons": {}
}