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After thinking about this a bit more, here's a theory on how it could happen:
So I first write a python script that would convert the BIN file into a list, which could look something like this:

with open(rom.bin, "rb") as file:
  for x in file:
     list.append(x)

And then I could copy and paste that into the Arduino file, and go through the list and write to the EEPROM.
(The list would not have 32k items, but the Arduino Code would first fill the entire EEPROM with EAs and then go through the machine code.)

Please feel free to point out any flaws with this plan.

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@TomNisbet
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