You are able to use emunand tool to create a backup of your emunand..
You will need to:
1. make a complete backup of your SD
2. Backup your emunand with emunand tool
3. launch gateway launcher
4. format emunand (this will completely format your SD
5. move all the files back to your SD and inject your emunand backup with emunand tool
I think thats all you need to do, I'm sure somebody will correct me if I'm wrong