How can I limit multiple shipping charges for orders from different locations?

[kbl155]

Hi, we're having issues with shipping being charged multiple times when products are sourced from multiple locations, we know that this is occurring because Shopify calculates shipping per location. We use Shopify POS for our bricks and mortar stores and they rely on having accurate inventory levels per location, so we can't manipulate the stock into one location to get around it. Is there a workaround or solution so that customers will be charged a maximum of one shipping charge per order? Happy to look at paid app solutions, it's a big enough problem.  The extra charges are preventing us from growing our customer base as our online stock is sourced across all store locations as well as our warehouse, and it's not cost efficient to offer free postage abroad or below our current minimum free shipping threshold.

We're on Shopify rather than Shopify Plus so cannot make edits to checkout, and we're based in Australia.

Assistance appreciated!