My 64GB microSD card (Transcend brand) I've used in my main N3DS for probably 4+ years suddenly went into a Read-Only state the other day. I found that certain games would crash the system upon boot, and Luma wasn't able to write screenshots (it thankfully informed me of the failed operations). Godmode9 wasn't able to reformat it. It's basically in a zombie state, alive, but dead. Until I buy a new card this particular 3DS can only really be reliably used as a DS or for its homebrew emulators which don't need to write files to function, from what I found. I assume that it's corrupted and unsalvageable.
As others have said, all SD cards will die especially if they've seen a lot of writes or abuse. I think me writing perhaps 30-40 screenshots via the Luma menu of a playthrough of a game a little while ago might have been the tipping point. The trusty card had a good run, and a 64GB replacement will certainly be a lot cheaper to buy today than 4 years ago.
Anyway, I'm glad the OP got a replacement as two weeks is a ridiculously short life. These things should never be considered long term investments.
You should use Checkpoint or JKSM to export your save data, and then backup the output of Checkpoint or JKSM. While you can backup specific files in the Nintendo 3DS folder, everything in there is encrypted and if something happened to your 3DS, you would need to decrypt anything copied from the Nintendo 3DS folder before you could use it again. Besides, everything is categorized by title ID and it's very inconvenient to navigate.
Also note that JKSM and Checkpoint can't touch GBA save data. You need to use Godmode9 to export that, if I'm not mistaken.
there's an app (can never remember the name of) that can mass backup gba saves or inject them. the original way can only do one save at a time. it's through godmode, yes. I think both might be. I'm not really sure how it works, but the mass injection/backing up method didn't exist when I did mine. yes, gba saves will appear on the sd card. I had to inject the save, backup the folder, inject another (which would replace the original), then drop the backed up folder back on the sd card. not hard, but it's tedious. that's no longer necessary afaik, but I have no experience with mass backing up using that app.