Oke I was a bit to fast with asking. I know now why the EERPROM gets erased. The fuses are set to erase the EEPROM at the chip erase chip prior to programming it. Correct me if I'm wrong :cold_sweat:
When looking at Sanquino's board.txt file:
atmega644.name=Sanguino W/ ATmega644P
Is see that the low_fuses=0xFF, high_fuses=0x9A and the extended_fuses=0xFF.
When I fill in these values at 'Atmel studio's AVR simulator - device programmin' I see that the 'EESAVE' option is not checked. When I check it the high fuses change to 0X92.
Is it OK to change the high fuses in the boards.txt file to high_fuses=0x92?