Hmm, I'm not sure I follow. Is this the sequence of events?
- Sketch sets eeprom flag and executes watchdog reset
- Bootloader starts running : detects and wipes eeprom flag, does three LED flashes, and starts communicating with AVRdude
- Communication is lost for reasons unknown, and AVRdude hangs
- Bootloader watchdog expires and bootloader resets itelf
- On this pass the bootloader does not flash the LEDs but immediately tries to start the sketch
- The sketch has been wiped, so nothing happens
How do you trigger the second sketch upload attempt?