We are also having this problem - been happening for a few weeks now. It's weird because it's happening on products randomly - things that were in the POS system the day before suddenly disappear the next for no reason.
Deleting and re-adding the POS app daily has helped fix known problem products, but it still occurs on other products.
This is often discovered with customers standing at the cash desk so deleting and re-adding isn't a feasible solution immediately. Sales associates are therefore selling under a "Custom Product" and then adjusting the inventory manually thereafter on the Shopify backend.
Of course this leaves it open to human error as staff will forget to do this from time to time and we will end up overselling the product online as a result. Additionally this will affect reporting statistics as Custom Products won't be listed under their appropriate tags and vendor information.
You working on this problem Shopify?