Your best bet is to re-bundle it correctly. I'm not sure if the amazonians can manipulate something on their side to help you out. Certainly the standard tools we developers have won't repair it.
Could you use ec2-download-bundle to pull the parts down from S3 and then use ec2-unbundle to recreate the AMI? I've never had to do that but from the description of the commands it seems like they might do what you want. If you can recreate the original .img file, you should then be able to use ec2-bundle-image with the correct ID and then upload it and register it.