DNS problem: query timed out

That's useful to know, thanks. If you take a look at one of the previous threads (During secondary validation: No valid IP addresses found) you'll notice there is a pattern of integrators hitting this error at 00:00, 01:00, 02:00 UTC.

There is a thundering herd effect at those times and you can make your renewal more robust by avoiding them.

There is also some advice on this at https://letsencrypt.org/docs/integration-guide/#when-to-renew .

Even though this kind of error is not ideal in general, it might be helpful to see whether moving away from that time of day gives you an improvement.

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