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if i recall, i read that there are certain bits that are set only during the programing phase, and data can only be changed when those bits are set.
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It's rather the other way around. The device can be freely copied, unless the security bit has been set intentionally.
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I am not quite sure where to start as this is my first time using an Altera product.
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Supposed, the boards have the JTAG pins of the device exposed to a 10-pin connector according to the Altera standard, you need an Altera programming adapter (e.g. USB Blaster) and Quartus II or an Altera-standalone-programmer (ASAP) installed.
Read-back the image ("interrogate") and writing it to another device in the programmer window can be done almost intutively.
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