Ok guys, I just had this exact problem tonight (Failed Bold 9000 software update, phone went completely dead and only had blinking red LED). Could not get blackberry desktop manager to recognize it. JL Cmder method didn't work as well, even after trying it at least 6x. If NOTHING has worked for you guys as was the case with myself, then try this below method, it will probably work.
Sorry for posting this huge post, but it won't let me post URLs' yet, it's actually copied and pasted from a link from a thread on here I found from 2008. I'm not sure if it matters, but I had my battery in the entire time. After the JL Cmder method didn't work, I was ready to write a check to my GF for a new phone b/c I was stumped. Thanks to this message board though, it's 100% fine now
What to do next if Jl Cmder will not connect and wipe
From BlackBerryFAQ
* Note: If you are connecting via a USB HUB then these instructions may not work. Try connecting via USB on a PC that is not using a HUB
Pre-Install Tasks
1. Disconnect the device from the PC
2. Download and install Desktop Manager and the Handheld OS to the PC (if they have not already been installed):
(you need to download the blackberry OS from RIM, I can't post URL's yet though) If you download desktop manager without downloading the OS it won't work. Also have to install the OS onto your computer once you download it, can't just load it directly into your phone from apploader.)
Command Line Tasks
1. Start a Command Prompt in DOS from the PC (Start >> All Programs >> Accessories >> Command Prompt)
2. Change the directory to: C:\Program Files\Common Files\Research In Motion\AppLoader
* If you do not know how to navigate to this directory follow instructions in 2a)
2a)
From C:\ prompt type:
cd \Program Files <hit enter>
cd Common Files <hit enter>
cd Research In Motion <hit enter>
cd AppLoader <hit enter>
3. Make sure Desktop Manager is not running
4. Connect BlackBerry to the PC
5. Enter the following command in the Command Prompt window:
loader.exe /nojvm
Installation
1. The Application Loader Wizard window will open
2. Click on Next
3. You will get a drop down list with the COM ports and one USB port entry
4. Select the one which says USB:UNKNOWN
******(MOST IMPORTANT!!!!!!!)****** If you do not see USB:UNKNOWN or USB:BBPIN, then follow instructions listed in a1-a5:
a1) Disconnect the device from the PC.
a2) Keep the Application Loader Wizard window open
a3) Remove the battery and put it back
a4) While the red led is on, reconnect the device to the PC. The led will only stay on for a few seconds
a5) When USB:UNKNOWN appears in the drop down list, you need to immediately select Next
5. The loader should now connect to your device and you will be able to reinstall the OS