Hi,
Michael: Indeed, it is hard to do reverse engineering of big code. But I do not agree that installation of external "security" chip such as Sentinel, Dallas-Maxim 1-wire button (DS1991 etc), is yet enough thing to protect board from duplication. This way, "not good people" will not do reverse engineering but crack instead. They disassemble code, locate checking routines and disable it. And so all these extra-chips come useless.

Bert: I see some other ways:
1) Use custom bootloader placed in user flash area which decrupts and re-flashes code. You have already mentioned this method yourself.

2) Use external programmed PLD. We use Altera which has JTAG and protect bits as well. It is programmed once with us and then we set protect bits. This way even if third-party people obtain MCU code, they still not be able to duplicate board because they do not know Altera internal configuration. As Altera is complex device and here it controls most board signals so re-engineering of it is not simple task.

3) Another expensive method. You said: we do not want the customer to have the HEX code .... Well, make updates with non-standard way. For example, it may be kind of "black box" which is connected to the custom connector of a board. What is placed inside it is your choice (=

Regards,
Oleg