Hi again. Yeah when using that Serial USB connection sketch, it is necessary to first disable the running cayenne-ser.bat script (with Ctrl+C), then upload any new code via Arduino IDE, then re-enable that script. At that point the Arduino should connect and show online again. This is because the Serial USB connection blocks the serial port that the IDE would use to communicate with the Arduino device.
I don't think you need to do anything special to disable the Serial Monitor in the Arduino IDE -- at least I have never done this despite using that sketch all the time. Just make sure you don't have any lines like
#define CAYENNE_PRINT Serial or
Serial.begin(9600); in your sketch, and comment them out or remove them if you do.
If it's still showing as offline and you've uploaded new code and restarted the cayenne-ser.bat sketch, perhaps the first things I'd check are are that COM15 is still the port the Arduino is connected to (you can verify this in the Tools menu of the Arduino IDE) and that your token still matches the dashboard entry that you're looking at.
Perhaps you can share the output from the cayenne-ser.bat script if you're still stuck trying to connect?