If you're looking at the flash hex file, it contains machine instructions. You basically need to figure out how to generate the assembly from it. Open it in AVR Studio and it will do this for you. I don't think you're going to achieve anything all that productive by trying to troubleshoot or reverse-engineer hex files directly. I imagine you could probably write the program itself faster than you could decode the hex and figure out how the assembly works.
If you're looking at EEPROM hex, it contains data in whatever format the user decided to store it in. There's no way to tell from the hex file itself what the data means or what the data types are.
- Ben
