[41south]

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The USB/serial connection is handled by the 16u2 I believe?
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Yes.

When removing the Diode we should be very careful, there are very small vias near the pad closer to the 16u2. I have already damaged one Meduino, this why I said to check the serial communications.

Regards

Fixed! Resoldered the usb connector and all is well again - which just goes to show that you should always check the simple things first 

Using the ICSP didn't affect the boot loader either thankfully so everything is 100% operational - and in 2-3 weeks I'll have a couple of spare Arduino boards 

[engolling]

I think you don't overwrite the bootloader if you use the special "sketch upload" function via ISP like 41south said.

engolling