I wrote a simple serial number genrator that fits my needs (it simply generates the number and writes it as serial number descriptor into an asm or c file).

Production programming is done by a small script. This script
- Invokes the serial number generator
- Invokes the Assembler or C-Compiler to translate the generated file
- Invokes the linker to link the project files
- Downloads the newly created hex file into the MCU

a) Fill the range to be replaced with 'FF' on the original firmware.

// string descriptor for serial number: ABC12345
{ 18,      // number of bytes in this descriptor
  0x03,    // identifier of the descriptor
  'A', 0,
  'B', 0,
  'C', 0,
  '1', 0,
  '2', 0,
  '3', 0,
  '4', 0,
  '5', 0 };
// string descriptor for serial number: ABCxxxxx
{ 18,      // number of bytes in this descriptor
  0x03,    // identifier of the descriptor
  'A', 0,
  'B', 0,
  'C', 0,
  0xFF, 0xFF,
  0xFF, 0xFF,
  0xFF, 0xFF,
  0xFF, 0xFF,
  0xFF, 0xFF };

c) Using the "Flash program utilities", overwrite the address in the serial number.

Anyway you need a 'serial number generator' program.
If a binary file can be generated, BIN2HEX converts it to a hex file.
"GENERAL: MAKING HEX FILES FROM BINARY FILES"

Our manufacturing team likes to use the MCUProductionProgrammer. Is there any advice or example that I can use to have it create a serial number that is compatible with USB descriptors in the firmware library? Specifically
code const BYTE USB_SerialStr[] = ...

Finally, I'm planning to move to a bootloader structure in order to upgrade firmware in the field. I would not want to reassign the serial number so it must reside in the bootloader space. Can I get any advice or direction on that?