After you sort out whatever or not your SD card is going bad, keep your Nintendo 3DS folder and backup the games saves + extdata with Checkpoint/JKSM save manager the first moment you get. Corrupted titles will require fresh installations; be warned reinstalling a game will overwrite whatever save you had in place.Thanks. Do I have to redo every single step listed there? A bunch of that stuff seems to concern writing to internal memory, and therefore wasn't lost with the SD data in the first place.
It would be wise to create a new (clean) SysNAND *.bin image for brick recovery purposes. First time CFW'ed 3DS users often fail to do CTRNAND Luma3DS where they mis-attribute black screen boot without SD card as a brick.
Yay, my advice is just redo everything in Finalizing Setup. If you use the CFW starter kit, you may want to selectively install titles found in the cias folder if you prefer homebrew apps on HOME Menu.