Possible to modify line items after checkout + before fulfillment?

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We would like to sell product bundles/kits (master SKU with individual SKUs contained within) for a fixed price, while also allowing coupon codes to be used.

Right now I have it working like so: when a bundle is purchased, the individual SKUs+quantities that belong inside it are added as line item properties (Product 1, Product 2, and so on)

This would work fine, but our items actually ship from multiple warehouses...so when we receive an order in ShipStation with a single line item and a bunch of other SKUs included as text, it doesn't allow us to easily split the order up.

So essentially what we're looking for is a script - or some middleware - to allow the entire checkout/payment process to occur with one SKU, and then automatically add the additional products as new line items BEFORE the order is actually sent to ShipStation.

Is there any way to accomplish this?