Syncing stock when stores have several locations
In Shopify a product does not have one stock number. Every location holds its own, and what a customer sees is the sum of the locations that store sells from. Sync between two stores therefore starts with a decision, not a switch: which locations are you sending, and where does the total land.
The sending side: which locations count
A store with a warehouse, two shops and a returns location usually wants to share the warehouse only. Shops sell from their own shelves, and a returns location holds goods that are not sellable yet. Sending the sum of all four would promise stock you cannot ship.
In StoreTwin you tick the locations that count, and their quantities are added up. Tick nothing and every location counts, which is the right answer for a single warehouse and the wrong one for the case above.
The receiving side: exactly one location
The total has to land somewhere specific. If the receiving store has several locations, choose the one that represents this stock - usually the location its orders are fulfilled from.
Choosing a location that does not stock inventory, or one that another system also writes to, is the quiet way to get numbers that never settle. StoreTwin marks locations that do not stock inventory in the list so the choice is visible.
Third-party fulfilment
Locations run by a fulfilment service behave differently: an app cannot set their quantities the way it sets your own, and they often represent stock you do not control. StoreTwin does not list them for selection, and counts them only when you leave the selection empty - the "every location" case.
If your fulfilment partner holds the stock you are syncing, that is worth solving before choosing a sync app at all: the source of truth is their system, not either store.
What changes when locations change
Adding a location to the sending store does not change anything until you tick it. Deleting a location that was ticked leaves a selection pointing at something that no longer exists, and StoreTwin says so on the connection page instead of silently falling back to everything.
Moving stock between locations inside one store is not a change in the total, and the receiving store should not move at all. If it does, that is one of the usual causes of drift worth checking.
Verifying per location
Compare like with like: the sum of the ticked source locations against the one destination location. StoreTwin's difference report is written that way, naming the variant and both values, so the check does not depend on remembering which locations were selected.