Yes the large EEPROM can be used for a different purpose.
Please make sure that the code area in the EEPROM is not altered. If the code area is changed, the device may not enumerate properly (if the descriptor code area is changed) or the device may enumerate and not function as expected on next time firmware load (C2 EEPROM boot).
You can check where the firmware code area ends in the .iic file. Open the .iic file in the an hex editor . The last bytes of the firmware is 0x80 0x01 0xE6 0x00 0x00000000. Note down the corresponding location address.
The following address after the end of firmware file can be used for your custom implementation.
Bulkloop firmware example:
Here the firmware code area ends at 0x0bb0.
The following area after the end address can be used.
I have used the vendax firmware to alter the EEPROM area after 0x0bb0.