The only semi-reliable way I've discovered is this:
- delay(2000) BEFORE Serial.start in the setup function
- Start the serial monitor IMMEDIATELY once you have programmed the board, and leave it running the entire time
- When you want to reprogram, hit the "Upload Sketch" button on the IDE without closing the Serial Monitor manually.
- Serial monitor closes automatically when you try to upload the sketch, and apparently the timing is perfect to allow the sketch to upload.
- Restart the serial monitor as soon as you get an "uploaded successfully" message.
It's almost as if any amount of serial output that is not monitored will induce the failure state.