I think this thread has strayed a bit from my original question. What I want to do is have the Cyclone power on and use the application config unless there is an error and then it would use the factory config as a default. But I don't know if this is possible and how I set the remote config address register in this case. The main question posed from my original post is:
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"All the remote update examples indicate the address register needs to be updated from the factory config, but is there a way to change this setting just the once from the Quartus software or similar? I need it to permanently point to the application address."
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Thanks
Brad