You're hitting a pretty common issue when syncing Shopify with QuickBooks Online through connectors. Most built-in connectors don't really handle a two-way inventory sync in real time. So, when inventory changes happen in Shopify due to a sale or an invoice in QuickBooks, they're not always properly updated without some third-party help.

Usually, the basic connector works one-way, pushing product and inventory info from one system to another every so often instead of actual real-time, two-way syncing. For that seamless two-way sync you need - where sales on Shopify update QuickBooks and vice versa - you'll probably need a solid third-party app like TradeGecko (now QuickBooks commerce) or Unify by Webgility. These tools are great at keeping inventory levels accurate across platforms.

This can be a bit tricky, though. I ran into this situation once, and trust me, setting up those solutions can be a bit time-consuming initially, but it really saves you from headaches later on. You won't have to worry about the nightmare of manual reconciling! Check out their setup instructions, and make sure you test it thoroughly. That debugging phase is when most folks figure out what's gotta be tweaked to fit their specific workflow. Good luck, and hang in there - it’s fixable!