Hi,
Shopify orders originating from Amazon always seem to have the Amazon Order ID in 3 places for me. The reference, the source_identifier, and in this case, note attributes.
As far as the line item itself goes, in the line item, there are properties and the ones I see are the Amazon Order Item ID, which gives a specific identifier that way.
You must get those too, and they have zip, zilch nothing to do with the Shopify API or its versioning. That is all due to the App used to interface Amazon to Shopify filling in those useful details.