Configurations:

• Multi-company & inter-company transactions (Synchronize Sales & Purchase Orders OR Synchronize Purchase Orders). The receiving/purchasing company determines whether they want to synchronize lots/serial numbers.
• Lot Numbers
• A new operation type for inter-company Receipts

Why do you need a new operation type?

A new field titled "Receipt Operation Type" was introduced with this new feature. It can be found in the Inter-company Transactions tab of the company settings (in developer mode). This operation type will be used to synchronize the lot/serial numbers.

The operation type should be a Receipt and have the Use Existing Lots checkbox selected. Once you set the new operation type on the field, select Synchronize Deliveries to your Receipts. This checkbox will help synchronize the lot numbers used on deliveries and use them on receipts. It is also a nice way of separating receipts from vendors from inter-company receipts. I'll use an example to show the configurations.

Example:

I have two companies: Company A and Company B. Company A manufactures household cleaners and Company B sells the items to end customers. Company B purchases the items from Company A. I have enabled inter-company transactions and created a new operation type in Company B: Receipts from Company A. The screenshots are below.

Workflow:

Company A creates sales order S00001 for Company B; the purchase order P00001 is made in Company B.

I'll confirm the PO and validate the delivery order in Company A: 10 units from Lot 123456 were shipped to Company B. Notice how the new operation type is used to create the receipt in Company B. 

Open the receipt in Company B, open the stock moves (or the detailed operations) and you'll see that  Lot 123456 has been automatically set: