1. Capture invoice 

Generate invoice to the location that you are transferring to, this will deduct your inventory and will increase your receivables. At the same time will result Sales price and Cost price to be zero (0) due to AT COST CHARGE between locations.

Transfer of inventory from Location 1 to Location 2

Location 1

Generate invoice at cost this will result:-

Dr. Receivables and Cr. Sales

Dr. Cost of sale and Cr. Inventory 

Sales will increase and Cost will increase at same rate resulting 0 impact on your bottom line profits.

Location 2

Generate Bill at cost this will result:

Dr. Inventory and Cr. Trade payables

Thus to eliminate inter-company transactions pass a Journal Voucher

Dr. Trade Payables and Cr. Trade receivables for both locations.

Dr. Sales and Cr. Cost of sale for location 1 

This will eliminate balances between the locations and will only leave inventory balances which are:

Dr. Inventory (Location 2)

        Cr. Inventory (Location 1)

Hope it solves something.