Is there a way to run manual DNS with expand and be able to update the DNS record once?

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No. 

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Please see How It Works - Let's Encrypt

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So what's the explanation then? If I add the first challenge to all domains, it works and doesn't ask me any more challenges. If I follow the instructions and only add it to the domain instructed, the challenge fails and I don't get asked any more challenges.

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@mattch You should be told the challenge value for the first domain. You press Enter to see the challenge value for the second domain and so on.

You can add them to the DNS as you go or wait until all 5 are complete and then add them all.

Give the authoritative DNS Servers time to sync and then press Enter to request the cert. Use a tool like unboundtest.com to verify them.

See my post #10. Isn't that how the Certbot prompts work for you?