Almost every time I turn off my 3DS it doesn't read the SD card so I gotta relink my PNID almost every time...
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Check for corrupted files on your pc and check your partition scheme. Also if it's above 128GB it could be causing issues.
The SD card is 8GB and it does not seem to have corruption. I personally think it's the reader on my 3DS because when I eject it and insert it again it works.
I see... could it be the contacts on the card being worn down?