I resolved this for sellers in this way. Hold on to your hats, you won’t believe it!
Yes Amazon functions with the ASIN and that screws up Shopify. So what to do! We throw Amazon orders into emails with the details. We know orders are being placed into Shopify by Amazon, but we cannot process them yet. So we regularly pull emails from Amazon. With those, we get the orders, the line items (SKUs) and we can start to rebuild Humpty Dumpty. At the end of playing with orders from Amazon, in emails, and then matching to Shopify, we can actually comprehend what has gone on, and get those orders to the third-party fulfillment center! And there is trickery there too as fulfillment with Amazon requires things to be tidied up there too.
So the moral of the story is this. I have a high volume client that sells a lot of stuff on Shopify and Amazon as sales channels. The Amazon to Shopify sales channel it pretty much hot garbage due to Amazon, and you can thus resort to emails to glue things together. So you write an App to sit in the middle and play monkey in the middle. It helps that the third-party fulfillment center also maps SKUs totally different from Shopify, and has no connection to Amazon items either. So we MAP things. And it all works!
So I am in awe of 2020! And how we solve modern e-commerce problems with frigging emails, because hey! Amazon and Shopify are so well-oiled together, like bros!
I am thinking Shopify has done all they can to ease the pain of this sales channel, but at the end of the day, there is zero-chance Amazon is going to let it function friction free, so they ensure they do things just one stroke off, one stroke different, boom. You’re in the pain zone!
Good luck to you! I felt your pain! I solved it with code, and you likely can too!