Things can go wrong at any stage with any device you use. This specially applies to the Mobile Flashing, Jailbreaking, Unlocking, custom firmware upgrading, etc. iPhone and iPod Touch are most concerned in this area as they hold enormous data and even a lay person nowadays is experimenting with it to gain more. The first thing every one will tell you is to make backup and trust me, you shall not neglect it. It will save you when you have no hopes remaining.
The iPhone and iPod backups includes settings such as network, widget, sound, display and other information like Texts, call logs and notes, etc. Most importantly it creates copy of IPSW i.e. your Firmware of iPhone and iPod Touch which can be used to restore it during bricked and dead phone situations.
There always been a confusion between Syncing and Backups. Apple published Knowledge Base Article for iPhone and iPod Touch which clears difference between backups and syncing and shows how to create a backup. It also details how to restore from a backup and then delete the unwanted backup files.
You can read the detailed article here: