Hi,
I'm 99.99% certain you can still have the flash memory of the device protected when using a bootloader. If that wasn't possible there really wouldn't be a market for encrypted bootloaders.
If you're looking for an encrypted USB bootloader there's an open source one from Diolan. If you're looking for "any" type of encrypted bootloade Brush Electronics seams to have it (Serial, USB, Ethernet etc).
If you're looking for a non encrypted bootloader which is free to use and distribute to your customer you can look at the ds30 loader (he also has a secure/encrypted version which is not free). Another alternative is Tiny Bootloader.
I've tried none of the encrypted ones but I have tried the ds30 loader.
/Henrik.




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