When first using this 3DS creates some management data on SD card. 3DS uses a separate directory than DSi: /Nintendo 3DS/<SomeID>/<SomeID>/Nintendo DSiWare. Filenames are same format as DSi: <titleidlow>.bin. The keys/format for these files are completely different from DSi. A DSiWare export(to SD card) from 3DS is ~0x3bc bytes smaller than an export from DSi.
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