Hello,
I just got a ArduinoISP (http://arduino.cc/en/Main/ArduinoISP) and I successfully used it to program my Uno (menu File/Upload using programmer).
Unfortunately, every time a sketch is uploaded the eeprom is erased and I loose any previously stored data...
Is there a way to prevent this behavior and only write to flash memory?
eeprom got erased, but I thought it was OK since the first upload sets the fuses;
programmed the board again.
And unfortunately the eeprom got cleared again...
Re-reading your post, I noticed that the high_fuses directive seems to be related to the bootloader upload.
So I wrote the bootloader to the board (expected to set fuses), then programmed it via ISP (overwriting the bootloader) and this time eeprom data were still there!