Answering your question, what I did is:You didn't answer the other question.
You should only be copying your old files back to a completely empty card. You don't want to just dispose of your old files, do you?
Also, h2testw is really the only way to be sure that a card is in fact okay. Otherwise you're just guessing.
https://3ds.hacks.guide/h2testw-(windows)
- no problems, everything working fine
- error copying a +4gb .3ds file into my 3ds SD card
- I copy everything from the SD and put it on a safe folder
- I delete everything from the microSD card
- I format it to FAT32 again (again yes, because I already did when I was CFWing my 3ds, that's why I say I was just being silly because the "too large file" is normal for FAT32 format)
- I copy back the files into the SD
- I turn on the 3DS with the SD inside and can't read it
- then I decide to do a good reformat and I put it back inside the 3DS but empty --> it does read it, so the reformat went nice
- I copy the files back again to my card and put it in the 3DS and there's no "can't read SD card" BUT there are no Homebrew app, no Universal Updater, anything from the CFW except TwilightMenu++.
- I decide to ask in GBAtemp.