There could be a more elegant solution, something built-in ExtJS, but manually checking for existing rows and deleting these from the original store, before adding the new one does work. Add these lines to the end of your fiddle code:

newStore = Ext.clone(store);
newStore.load({addRecords: true,
    callback: function (records, operation, success) {
        if (!success) return;
        Ext.Array.each(records, function(record) {
           const existing = store.findRecord('name', record.get('name'));
           if (existing != null) {
               store.remove(existing);
           }
           store.add(record);
        });
    }
});

I solved this issue creating overrides:

Ext.define(null, {
   override: 'Ext.data.ProxyStore',

   privates: {
      createImplicitModel(fields) {
         //const me = this;
         const modelCfg = {
            extend  : this.implicitModel,
            statics : { defaultProxy: 'memory' }
         };

         if (fields)    modelCfg.fields = fields;

         // Add
         if (this.idProperty)    modelCfg.idProperty = this.idProperty;

         const model = Ext.define(null, modelCfg);
         this.setModel(model);

         const proxy = this.getProxy();

         if (proxy) {
            model.setProxy(proxy);
         } else {
            this.setProxy(model.getProxy());
         }
      }
   },

   load(options) {
        if (typeof options === 'function') {
            options = { callback: options };
        } else {
            options = options ? Ext.Object.chain(options) : {};
            options = {...options, ...this.loadOptions};
        }

        this.pendingLoadOptions = options;

        if (this.getAsynchronousLoad()) {
            if (!this.loadTimer) {
                this.loadTimer = Ext.asap(this.flushLoad, this);
            }
        } else {
            this.flushLoad();
        }

        return this;
    }
});



var store = Ext.create('Ext.data.Store', {
    fields: ['ids','name','email', 'phone'
    ],
    autoLoad: true,
    loadOptions: {addRecords: true},

    idProperty: 'name',

    data: [{
        'ids':1,
        'name': 'Lisa',
        "email": "lisa@simpsons.com",
        "phone": "555-111-1224"
    }, {
         'ids':2,
        'name': 'Homer',
        "email": "home@simpsons.com",
        "phone": "555-222-1244"
    }],


    proxy: {
        type: 'ajax',
        url: 'data1.json',
        reader: {
            type: 'json',
            rootProperty: 'items',
            totalProperty: 'total'
        }
    }
});

Ext.create('Ext.grid.Grid', {
    title: 'Simpsons',

    store: store,

    columns: [{
        text: 'Name',
        dataIndex: 'name',
        width: 200
    }, {
        text: 'Email',
        dataIndex: 'email',
        width: 250
    }, {
        text: 'Phone',
        dataIndex: 'phone',
        width: 120
    }],

    height: 200,
    layout: 'fit',
    fullscreen: true,
    renderTo: Ext.getBody()
});

// store.load();
//store.load({addRecords: true});  // Keeps Homer but duplicates data

Please see fiddle: https://fiddle.sencha.com/#fiddle/3h2v&view/editor

This allows you to use any field and field type as ID, it works with autoload on.

If you only want to use the id field as ID and it being numeric, then this should work: https://fiddle.sencha.com/#fiddle/3h15&view/editor