Man, you don't need to complicate the things, as stated at first FORMAT YOUR SD FAT32 you will be less prone to corruption.
If you don't want to loose anything is simple: MADE A BACKUP
For the Emunand on a Raw partition use the great tool
EmuTool and for the exFat partition, just copy the files to a safe location.
Use fat32format (the gui version is better for noobies)
http://ridgecrop.co.uk/ and then restore your files. if you don't touch anything besides the formatting of the first partition your emunand should get untouched and works normall, but if you messed it (normally by not reading) you can restore using EmuTool.
Easy, on my 240 GB SD Card a full backup and restore (almost full) took me 30 minutes.