Hacking Games and apps missing after upgrading microSD card

[t1op]

I have a New 3DS XL. I am on 11.5.0-38U. I have boot9strap and godmode9 both successfully installed.​

It came with a 32 GB micro SD. I was running out of room, so I decided to upgrade cards.
I moved all of the data to a 64GB card, but, even though formatted to FAT32, the 3DS wouldn't read it.
So I copied everything to hard drive. I tried to format to FAT32 again. Couldn't. Said the drive was in use.
So I formatted to NTFS. Then I formatted to FAT32 successfully and the 3DS could read it. I copied everything back to the 64GB card.

Now when I boot up, all games except 3 DSiware games are missing.
The Homebrew Channel and other homebrew are gone, except TWL Slot-1 Launcher.
FBI/Safety Warning also doesn't work.

What went wrong? Is there a way to get everything working again without starting from scratch?

 

[TurdPooCharger]

1. Reformat the 64 GB card to FAT32 + 32 KB using guiformat.
2. With nothing on the card, check using H2testw in a Full Write + Verify test.
3. Report back what your result states. Take a screenshot if you're not sure how to interpret what it means.

Edit - Do the test anyway. The DSiWare games are installed on your SysNAND (internally on the 3DS) or EmuNAND (which is emulated) on the SD card if one was setup.

 

[t1op]

Thanks for the attempt. Didn't help, though. Tried two cards. Same problem. Nothing wrong with the cards.
I did get things working again, though.
On one of them I copied everything but the Nintendo 3DS folder. I inserted it and let the system create a home management folder. I copied everything but the management folder back on. Then I copied the files from the old management folder into the new one and everything came back, although outside of the created folders.

 

[Quantumcat]

Thanks for the attempt. Didn't help, though. Tried two cards. Same problem. Nothing wrong with the cards.
I did get things working again, though.
On one of them I copied everything but the Nintendo 3DS folder. I inserted it and let the system create a home management folder. I copied everything but the management folder back on. Then I copied the files from the old management folder into the new one and everything came back, although outside of the created folders.

Sounds like you had corrupted home menu data