Hi @zach8, I’m continuing our conversation here as my reply is related to the Square Online Checkout plugin.
I’ve tested processing a payment using the Create Order Payment Link action using a Catalog/Inventory item in the Line Items List. I can confirm that this did reduce the item’s stock in my test account.
Feel free to reach out to Square Support or check their documentation if you’d like to understand how their APIs work. Our Square plugins are available to help make it easy for you to integrate your Bubble app with the Square APIs.
I hope this helps 
Phill