We are developing a headless CE 6.0 device (almost identical to the evaluation board AT91SAM9260EK from Atmel) with ethernet connection.
We can access the devices via the internet, but the devices can be located on the other side of the world. So it should be possible to upgrade remotely.
How can we upgrade the kernel (NK.BIN) ?
We can easily write a user program that downloads and stores the new NK.BIN on a disk (flash drive). But how can we flash this new NK.BIN into the flash chip?

I'd have the boot loader copy the new image, or be capable of booting from two images, usually the newer one, and that you can validate the image.

If the code is not running from NOR, you could probably also overwrite a fixed address image in flash from user space, or with the help of a driver. I'd probably want to have two images, so as to reduce the chance of bricking a working one.

If the board has an MMC card, you could have a boot loader pull update content from that also.

Anyway you need to think of strategies, and potential failure points, so you don't brick devices in the field. And then you need to test your mechanism thoroughly.