I'm not seeing anything in the code path for order creation calls that would suggest the shipping address could be set as the customer's default address if a customer_id is present. Do you have more details to suggest this was the case? The raw request that used to cause this behaviour? A sample order id where this happened?
If there was a breaking change to the API, it absolutely should have been tied to a version to give a proper deprecation period.
In general, I'd recommend explicitly including the fields you want to be included in the order.