No system update from Nintendo could fix it because the vulnerability wasn't in the software; it was in the immutable hardware (the BootROM). The only way to remove boot9strap from a 3DS is to physically replace the CPU.
Boot9.bin is the name commonly used in the 3DS modding community for a binary dump of the 3DS SecureROM (often called Boot9), the device’s earliest-stage boot code stored in read-only memory. Because Boot9 runs before virtually all firmware protections and has access to cryptographic keys and hardware initialization, its contents are extremely powerful: a Boot9 dump can enable full, persistent low-level control over a console that bypasses signature checks, secure boot, and many software-based protections. Boot9.bin 3ds
: Modern CFW like boot9strap (B9S) is named after this bootrom because it exploits the boot process at this very early level, granting full control over the system. Troubleshooting Missing Files No system update from Nintendo could fix it
Unlocking Your 3DS: Why the File is Your Golden Ticket If you’ve spent any time in the 3DS homebrew scene, you’ve likely seen the name Because Boot9 runs before virtually all firmware protections
Because it contains console-specific keys, you should never share your unique boot9.bin online. It's for your eyes (and your 3DS) only. Pro-Tip for 3DS Owners