Update in forEach on mongodb shell

To get what you want you will need a few things:

t.forEach(function( aRow ) {
    var newFields = [];
    aRow.fields.forEach( function( aField ){
        var newItems = [];
        aField.items.forEach( function( item ){
            var aNewItem = { item: parseInt(item), ref: 0 };
            newItems.push( aNewItem );
        } );
        newFields.push({ _id: aField._id, items: newItems });
    } )
    aTable.update(
        { _id: aRow._id }, 
        { "$set": { "fields": newFields } }
    );
});

So basically you need to “re-construct” your arrays before updating