It's unknown what code handles the below behaviour(NIM, AM, or AMXPXI).
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When finalizing title-install of already downloaded Old3DS system-titles to a New3DS NAND image with New3DS NATIVE_FIRM, the end result is that the New3DS version (TID-low bitmask 0x20000000) of those titles gets deleted.
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When finalizing title-install of already downloaded Old3DS system-titles to a New3DS nandimage with New3DS NATIVE_FIRM, the end result is that the New3DS version(TID-low bitmask 0x20000000) of those titles gets deleted.
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It's unknown where this behaviour is implemented (might be NIM, AM, or AMXPXI).