Messing with Hex is a useful thing.
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We wrote our own InSystemProgramming software. The C program takes the product's released version hex file, personalizes it, and then FLASHes the final code just before shipping.

We add data like serial numbers, calibration information, customer fields and encryption keys for each unit we sell without recompilations or other serial handshaking. The program just appends the information in INTEL HEX format and sends it to the FLASH.

-Jay C. Box