The protection of IP in embedded appliances is a huge issue for many corporation, especially with the amount of competitive reverse engineering and market pressures. In my experience, there is no exact way to protect your "hardware" invention 100%. You can keep "honest people honest", but that is it... GREAT now your scared...
For example, you may be able to store information on soldered flash, you might even encrypt it, but the key to decrypt it has to be read into RAM at some point - therefore its already broken. Flash can be removed and read, onboard buses on PCBs can be tapped into, CPLD/JTAG access and source code can be reversed quite well using software like ADApro.
OK so what can I do to protect my organization's intellectual property???
You can try to protect it with IP patents, cover it with glue (like the automotive industry does for its PCMs; it also doubles as heat protection), but remember, one of your biggest threats is persons who work on your software & the infrastructure supporting its development (keep it secure). The goal is to make sure that its difficult enough for a third party to gain access and understand; however, this is not security by obscurity.
If you make your system time-consuming for an attacker - they may move onto other easier targets which equates to protection by difficulty. However, remember state agencies and some organizations have extensive budgets and unique tools.