Best practices for production programming of data/NAND flash devices
The trick here is PogoPins (Wikipedia)

Basically you make a jig where you drop the board in  often descriped as a Bed-Of-Nails In-Circuit Tester/programmer, and it's then flashed without having to deal with the connector-mating aspect of the jtag interface.

LadyAda did a tutorial, and so did SparkFun