Basically, we need a setting that allows you to say "only pull orders from Shopify that are at least XX minutes old". Preferable at least 30-60 minutes old, in my case.
We use an app called One Click Upsell, which basically presents customers with an opportunity to add a special deal to their order after they've already checked out. It comes in as a 2nd transaction, but the app automatically merges the 2 orders within Shopify. There's a decent likelihood that we could sync our orders and pull an order into ShipStation in that window of time between when a customer has completed their initial checkout, but not yet added the upsell. Because ShipStation won't re-pull that order, we would never know that that order had been modified after the sync.