In the application, you can use the "Change #" option in the customer record to update the customer record to match that of the customer you wish to merge it into.
For example, if I have customer 999 and want to merge it into customer 012815, I would open customer and pull up customer # 999. I would then click "Change #" in the top toolbar. I would leave 999 as the old customer and enter in the 012815 customer I want to merge 999 into.

You will get a popup asking if you would like to merge them. Select yes to merge the records together into the "new customer #" you had selected. This will merge the customers for you.

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