AVRDUDESS prevents you from wiping the EEPROM side of things when you press program.James,
The fuse setting of the QCX is what should stop EEPROM erasure.
In view of problems seen recently it may be worth checking the fuses first.
But I suggest a beginner does not use the "Program!" button.
The "Go" button under the Flash box only writes the .hex, nothing else.
73 Alan G4ZFQ