Stop using RXTools. RXTools is long dead and the actual RXTools are highly unstable.After looking through the rxtools menu's a long time ago, I pressed one option (think it was in the same menu with something related to friend codes) and after rebooting, my 3ds had a black screen and blue light. I can access recovery mode and updated all the way from 7.0 to 11.2, but it still has the same issue. I don't know the options that were in the menu, so I do not know the option I used to brick my 3DS. Also, this happened before I got to backing up my NAND. Could anyone post a list of menu options of rxtools? It might shed some light on what caused the issue.
Setup a new CFW and use Decrypt9
http://gbatemp.net/threads/faq-what-cfw-is-best-for-me.428509/