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The cron should run always.

They have a rate limit for the amount of renewed certs. This doesn't apply if you don't reach their servers or don't get a cert.

But if you have a problem with a CA just switch to another which supports your bot (e.g. acme compliant CAs).

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Right, if your scripts can screw up, after the CA issued a certificate, their costs are locked in, (and thus Let's Encrypt rate limits apply here) and you should make effort to be able to recover the key and certificate if you fail rather than start over.

The private key only you have, so that's the thing you most need to avoid throwing away over and over due to a bug. If you lose the certificate, that's a public document, you can just get another copy manually if necessary.

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