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One way to reprogram the EEPROM with .iic file is by disconnecting the I2C lines (if possible) connected to the existing EEPROM (pull ups on SDA and SCL should still be present). The FX2LP will boot up with a "No EEPROM device" and gets detected in cyconsole. Then connect back the EEPROM to the device and program it using Cyconsole.
Please refer to Recovering Corrupted Boot EEPROM of FX2LP – KBA222693 for alternate method.
The EEPROM and I2C lines can not be disconnected, it is wired on the PCB board. I soldering 24LC128 and solder another EEPROM chip on our PCB board.