App for managing batches for delivery?

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We want to migrate a bakery business with local delivery from a custom e-commerce solution that I built using Ruby on Rails and Stripe onto Shopify. However the way Shopify allows you to input quantities of products does not meet the merchant's business model. Can anyone recommend a solution that already exists in the app store or is it better if I make a custom app for our merchant? Read on to get a bit more detail.

The bakery is owned by my younger brother. We bake batches of breads each week and take orders for them until a order-by cutoff deadline. The customers go on the website and order the breads they want and choose and associated delivery date for the batch they have chosen. However we allow multiple batch orders to be placed at once, so you could order a large sourdough for this weekend and another for next weekend, and they would go through in the same order but behind the scenes the inventory quantities would be subtracted from two separate batches which correspond with those delivery dates.

The way Shopify's system is, you cannot do this. This seems like a solution that a lot of merchants selling perishable goods in batches would need. Can anyone comment on this pain point and how people get around it?