Nintendo have update the Nintendo 3DS Firmware to V3.0.0-5 that blocks many flashcard from working . But it does not seem like all flashcards have been affected. Please check the list below to see if you’re affected:

Confirmed Working on 3DS V3.0.0-5
—  confirmed to be compatible with the firmware 3.0.0-5 by manufactures

• R4i Gold 3DS Card (r4ids.cn)
• R4i Gold Plus (r4ids.com)
• R4i SDHC 3DS Card
• R4i- Gold Pro Card (r4i-gold.com)
• Gold3ds Card support 3DS 3.0.0-5 J ( gold3ds.com)
• R4iTT black & purple (r4itt.net)
• R4iDSN (r4idsn.com)
• Supercard DSTwo (Firmware 1.13)
• Supercard DSONEi
• CycloDS iEvolution (in DSi Mode)
• Acekard 2i
• Ace3ds Cards (ace3ds.com)
• M3i Zero

Confirmed Non-Working on 3DS V3.0.0-5

• R4i SDHC V1.4.3 (r4i-sdhc.com)
• R4iSDHC RTS Card (r4isdhc.com)
• R4i -Gold Cards (r4i-gold.com)
• EZ Flash Vi
• DSTTi

Regardless,If your flashcard is listed under non-working, I recommend that you do not update your 3DS until manufacturers have fixes for the new 3DS 3.0.0-5 firmware ready.