According to GoNintendo, if a gamer decides to use flash cards for playing illegal, downloaded ROMs, then say goodbye to functionality on your 3DS. Nintendo will likely brick the handheld gaming console using a firmware upgrade down the line.
Nintendo hasn't made an official statement regarding this future action, but GoNintendo cites the following passage from the 3DS Terms of Agreement:
In case if you use equipment which is illegal or unapproved by Nintendo or if you do customization which is unapproved by Nintendo, there is a possibility that Nintendo 3DS become non bootable by system update.
So don't say we didn't warn you.
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