Sales Receipt Collisions between QBO and Shopify

We have a Shopify Store we started recently, but have been using Quickbooks for a long time for our book keeping. After integrating, when Shopify sends over Sales receipts, then sales receipts and invoices in QBO automatically start to follow the Shopify numbering system.

The problem with this is that the integration is not two ways. So next time Shopify creates an order and sends, it will be a duplicate of something made directly in QBO unless we change it each time manually.

The only thing QBO could tell me to do was to turn off the automatic numbering system, but this doesn't make the workflow any better because we would have to start remembering what to type in every time for an invoice number vs just fixing it when a Shopify order comes over.

If Sales Receipts and Invoices could be places on separate numbering systems that would work, and we would simply use invoices for payments - but they seem to follow the same numbering system.

I tried adding a Prefix/Suffix in Shopify for orders, but QBO simply picks up on that as well.

I imagine paid integration apps probably fix a lot of problems, but does anyone know a workaround for this particular one? We don't want to jump straight to having to pay for something else.