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The option to save EEPROM data during a program download is controlled by the EESAVE fuse.
The default fuse settings recommended in the Flowcode documentation (Chip -> Configure menu) select the external crystal oscillator and cause all additional features to be disabled.:
0x0, 0xdf
0x1, 0xff
It is possible to use alternative settings (with reference to the manufacturer's device data sheets) to configure the device differently. Note: Selecting a clock source that is not available to the device will stop chip operation and prevent it from being re-programmed in ISP mode.
There are several websites that provide AVR fuse value calculators
In the Flowcode configuration window, the first value in each pair is the fuse byte identifier, the second value is the fuse setting:
Start AVR Studio 4, conntect to the ATmega, then go to the Fuse Dialog and first READ the fuses, then set the EESAVE option and programm the fuse-settings.
Now Flowcode does the Flash-programming without erasing the EEprom.