Mega 2560 connected to Vista.
Basic Blink sketch uploaded with 250 millisecond watchdog code added.
Pin 13 LED now flashes rapidly.
Sketches will not upload.
Releasing reset while trying to upload doesn't work. LED flashes fast as soon as reset button is released.
AVRdude responds with timeouts.
It will go into DFU mode and USB driver installs but Flip or AVRDude cannot open/find USB device.
Disable "AUTO RESET" did nothing.
What do I need to do to get this Mega working again?
I've done the same thing when testing if my mega1280 bootloader could handle short WDT timeout values. The test worked fine on all my 328P based boards using the Uno bootloader but 'bricked' my mega board with the same symptoms that you are seeing, fast switching of pin 13 LED.
The problem is that the bootloader in your mega does not disable WDT interrupts when it first starts up, so it gets locked up in a constant reset/start bootloader/reset loop condition. The only solution is to reburn a bootloader on your mega board using a hardware ICSP (which can be another arduino board running the arduinoISP sketch). Reburning the bootloader will restore it to operation but will not solve the ability of handling WDT short duration interrupts unless you locate a mega bootloader HEX file that has been patched to solve that problem, the default mega bootloader in even the current arduino IDE still does not fix this flaw.
This problem has nothing to do with the USB serial converter chip and you should not mess with it's firmware to try and fix this problem, unless you messed it up in attempting to fix what is a mega1280/2560 bootloader bug.