You said earlier that a high impedance load is no problem. And that an LED is such a high impedance load.
But you also indicated that a diode isn't a high impedance load. Or at least, that connecting a diode in series with a low impedance load wouldn't allow you to connect the low impedance load.
Does high impedance mean low resistance?
You also just said the pins are set to an input state which is high impedance. Does that also mean low resistance? I thought the input state was one where they went to ground via a large resistor, which is why you can use that state to charlieplex... because electricity won't flow easily.
But then you said:
Then the boot loader takes over and initialises pins 0 and 1 to use serial communication. So the TX (pin 1) is an output set high and the RX (pin 0) is an input. The Serial / USB chip is connected to these pins through a 1K resistor so it has a limited capacity for pulling pin 0 low if another load is attached to it. Similarly pin 1 is connected through a 1K resistor, if this has a load on it then it might not be able to drive the serial chip to the required voltage levels.
Given that it's been said leds are high impedance, and the pins are high impedance, and that it was said high impedance loads aren't a problem for the serial pins, why does it seem here like you're indicating that the setup I descibed will interfere with uploading the sketches?
I'm totally confused now. 