Is the bootloader update due to corruption of the existing one?
Is the diode a replacement or board revision/mod?
No. If the bootloader were corrupt you would not be able to upload.There is a bug in an earlier version of the bootloader. What I remember is that on power-up the bootloader would corrupt the application area. But your board would have had to have been manufactured several months ago.Details about the latest bootloader...http://arduino.cc/forum/index.php/topic,64105.0.html
That's something you will have to decide. It is my understanding that folks have successfully modified their boards. But, it is also my understanding that the Arduino folks stand by their products which means you should be able to get it replaced if it has a problem.Diode details...http://arduino.cc/forum/index.php?topic=64256.0.html