We believe the safest way to run Magic Lantern (or any third party camera control software) is to use custom modes - in these modes, Canon code does not save user settings to NVRAM. We did encounter such problems during development, but we were able to recover from them.

We consider this a design flaw in Canon software. Imagine that your config file gets corrupted and you can't just delete it and start from scratch. Even developers of USB control software, who use Canon's own SDK, agree with this.

These programs use the same API for changing camera settings (properties), and Canon code does not always check the validity of the settings before saving them to NVRAM.

The same risk is present if you use third party software for USB remote control. If Magic Lantern would set incorrect values for certain settings, this may cause the camera not to boot (even without ML). Magic Lantern does not replace Canon code (which is stored in ROM), but it does change the settings (which are saved to a non-volatile memory). Therefore, we can't be certain that it's 100% safe. Magic Lantern was created by reverse engineering an undocumented system that controls hardware.

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