These are general CFW/Cart/Hacking caveats on the 3DS platform that modders, hackers, and pirates should read and understand the implementations before commencing on their hacks journey.
- CIA files require installation to the system, either Emulated (EMUnand) or System (SysNAND) NAND. Installing directly to the SysNAND could kill your 3DS should power be lost or the CIA file be corrupted somehow. While the risk is low, installing CIA to EMUnand only is recommended and SysNAND installs should only be done once you have a NAND backup.
- Downgrading 3DS console to 4.5 may break your game saves in SystemNAND as save encryption changed in FW 6.x. Downgrading isn't recommended any more and Roxas75's MSET downgrade should be used instead.
- Game cart updates will NOT upgrade your webkit version, only online updates will.
- New 3DS cannot boot an EMUnand version above firmware version 9.5. This may become a problem as newer games use newer SDKs which require higher firmware versions. The possibility to manually update system files is there but has yet to be demonstrated. CIA installers like FBI/BBB/DevMenu can be used along with a NUS-downloaded firmware (no longer available though Nintendo) to manually upgrade a 3DS EMUnand to this verion firmware.
- Nintendo has introduced a new game encryption (AC and FE:IF only as of 22/SEPT/2015) which may render future releases and online play of 3DS ROMs from carts like Gateway and Sky3DS impossible. Here is more info It seems CIA files lack the required header data for this encryption and are not effected at present.
- When a System is setup with EMUnand, the user should backup their EMUnand using EmuNAND Tools and then format their SysNAND to unlink them. You are essentially making an identical clone of the systems NAND on your SD card. When you install an eShop title or CIA to either NAND, the other one will also see it and you will have constant gifts to open.
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