I mistakenly thought that re-assigning all entries on an association would cascade a save! on the owner of the relationship to the depended models if they were dirty. Turns out, nope!

whoops.rb

class CountsInventory
  def count_inventory(store)
    Inventory.find_or_initialize_by(store: store).tap do |inventory|
      inventory.assign_attributes(date: Time.zone.now.to_date)
      inventory.items = count_items(inventory) # Updates which items are associated, does not cascade save to them
      inventory.save!
    end
  end

  def count_items(inventory)
    Item.where("stock > 0").find_each do |item|
      InventoryItem.find_or_initialize_by(inventory: inventory, item: item).tap do |inventory_item|
        inventory_item.assign_attributes(count: item.stock) # Will not change on subsequent runs!
      end
    end
  end
end

store = Store.first
Item.create!(store: store, stock: 2)
CountsInventory.new.call(store)
inventory.items.first.count # 2!

Item.find_by(store: store).update!(stock: 4)
inventory = CountsInventory.new.call(store)
inventory.items.first.count # 4, good!

inventory.items.first.reload.count # 2! Oh no!

FYI, this was fixed by setting autosave: true on the has_many association!