Yuck! Two things came to mind as I was reading your post:
1. It sounds like a condition when a battery dies during the firmware upgrade which I'm sure can't be good. Have you checked your battery or do you have another one to try?
2. Your firmware download is corrupt and choked at the point of failure. Or along the same line, your CF card is corrupt or needs formatting/replacing.
Assuming you can get power back to your camera, download the firmware again and place onto a different card--might be worth buying a quality card if what you have is questionable. Ideally the card needs to be formatted with your camera and not your computer if that is possible at this point.
Some other things you have probably looked at but just in case you haven't:
- Is it possible there is something in your battery chamber, a shread of paper or something which is blocking one of the contacts? Just maybe it was coincidentally that you lost battery connection when updating
- Is it possible you have a bent or damaged pin in your CF card socket. Again this would be a coincident but since the card was just pulled and reinserted prior to the failure maybe.
- Check your battery with a multimeter.
- Carefully clean your camera's electrical connectors.
- By all means call Canon
Please keep us posted on the outcome, we would love to hear the cause and solution.