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Have you tried the instruction set simulator? Not sure that would help in you're case but if it did then you could stay hardware independent until integration time. Then if things don't work after the hardware and software teams can have the usual battle-royal hehe.

If you take Daniel's advice that might be best if you already have the lan interface available and you can convince the person in charge of the hardware design to include it with the lan core supplied with NIOS II. So you'd have a little loader that you keep in the CPU and then you blast the program across the lan connection, and when that's complete you're program jumps to it instead (or have it on a button if it's available to you).

Atleast that solution does not modify you're code in any way, and the extra hardware can be removed after.