Hi traxman,
It's not possible to verify the EEPROM contents when using "Write Latest Compilation Through USBi". This is because the check compilation function uses the USBi, and the USBi isn't directly connected to the EEPROM in your case, so unfortunately there's no way for it to directly access the EEPROM's contents.
However, I think it's highly unlikely that the EEPROM data would be corrupted during the "write via DSP" function.