This is how the process functions: When products are fulfilled from multiple locations, the shipping rates are combined.
Even an app cannot resolve this, as Shopify calculates shipping for each location separately and then adds them together.
On a separate note, when you ship from multiple locations, it may incur double costs since you need to process orders from each location. Isn’t that the case?
This is a known issue and multiple merchants are facing this issue. Hopefully Shopify does something about this.
Meanwhile, a hack which worked for some of our client (very small scale merchants) was that they created a new dummy location and marked that location to be the only location from where shipping is allowed.
And then they manually updated the respective locations with correct inventory numbers at the end of the day to reflect the real inventory count.
It’s not an ideal solution but a workable solution.
We seemed to have found a solution for this in our app ShipMagic. Using our app’s shipping customization feature, you can setup rules to only charge one flat rate even if there are items from multiple locations present in cart.
Moreover this solution works on all Shopify plans including the Basic plan. You can install the app and reach out to live chat support for help on setting up the app.
My last two orders (mixed locations) have only charge one carriage. I might be wrong, but haven’t needed to refund a duplicated carriage charge for these two.