It doesn't have anything to do with a third party plugin. It also throws errors when using it with standard woocommerce. Like I said, when you add a product to the product catalog, add it to an order, then remove the product from the catalog and then try to change the order, it throws the same error.
This is just using your plugin and Woocommerce, so it does give an error.
It's a very easy thing to fix really, you should only add a check in your code to see if a product does exist before you start doing any operations on it.
Hope you can come with a solution soon!