You should be able to fix it yourself but if you can get the Apple tech do it anyway then just do that.

Start iTunes and plug the turned on iPod in. It should detect that an iPod has been connected and offer to do a restore. You'll probably have to resync everything that was on there though.

The majority of the firmware files in an iPods are actually kept on the HD and there is a recovery mechanism so if it does get corrupted you can fix it.

I don't see how there is a conflict between iTunes and Emplode though. Maybe if iTunes moved files into its own directory structure whilst Emplode was running...

Restoring iPod to factory settings