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You might be able to make an encrypted version of the configuration that programs the EPCQ. It would need to use the same key that is programmed into the FPGA. I've never used the encryption feature, so I don't know any details.
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thank you for the tip.
Based on your idea, I think I could do like this: I make a second board with the FPGA not tamper-protected. This can be called as a "programmer". Using it I can write a new EPCQ with encrypted configuration data. Then I replace the old EPCQ on the target board with the new one. To make the work easier, the programmer could use a chip socket for EPCQ.
This approach is more complex than on-line programming, but it is any way a good solution.
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