Updating firmware should take only a minute or so, anything longer anything longer and it's not happening for some reason.
What version of OSX were you running? Were you using the new (Version 2.05) Mac flash tool- it sounds like you were? This was just uploaded to the Atomic site within the last few days.
Am I understanding correctly that the Cobalt is stuck showing the green "Connected to PC" message, you can't back up? It won't go to sleep in that screen. The first step you would see with an update happening is the screen going blank- unplugging after that happens will cause the update to fail, though there are recovery instructions on the Atomic site. Recovering from a failed update just requires another step. Those instructions are at the bottom of the page here:
Atomic Aquatics Cobalt Software
I would unplug, quit the Mac application, and re plug and restart the process. See if the Mac application recognizes the Cobalt. You will want to make sure the cable and adapter are secure, and it wouldn't hurt to try a different USB port on the Mac. If that doesn't work, PM me and I'll give you detailed instructions for a battery (hard) reset.
Ron