@Usagyuuun, maybe I should be more careful about telling you what to specifically delete.
- Go in the sdmc:/Nintendo 3DS/<ID0>/<ID1>/ directory and delete only the dbs and title subfolders.
This is in case you still have any important
extdata. There's also the
Private folder voice recordings from Nintendo 3DS Sound and photos from Nintendo 3DS Camera.
Leave everything else on the SD card intact.
Edit - You can copy & paste (or update) your current collection of 3DSX apps,
boot.firm,
boot.3dsx, etc. with the newer set from the CFW starter kit. Just make sure to keep files that are personal or important to you like the themes and roms.