Magento2 – Stock Inventory Not Being Updated

This is actually a feature of Magento. This allows you to set a product "out of stock" (if you have reasons to) independent from the product qty. The simplest solution would be to modify the cron that sets the product quantities to set the 'is_in_stock' flag on the inventory item to 1 it the qty is 1 or above. Maybe you should post some code from your cron and we can help you change it to fit your needs.

Why you use external cancel functionality to load model each time, Magento Provide cancle() function.

Try This code to cancel order:

if(!$order->canCancel()) {
    throw new Exception('Order cannot be canceled anymore.');
}
$order->cancel();
$order->save();

I give you such idea to use cancel() like:-

$orderModel = Mage::getModel('sales/order');
$orderModel->load($orderId);
if(!$orderModel->canCancel()) {
$orderModel->cancel();
$orderModel->setState(Mage_Sales_Model_Order::STATE_CANCELED, true);
$orderModel->save();
}

System->Configuration-> Catalog ->inventory->stock options->Set Items' Status to be In Stock When Order is Cancelled change this value to "No".

You can also stop to decrease the stock quantity on order placed: System->Configuration-> catalog -> inventory->stock options->Decrease Stock When Order is Placed