Can not find issuer 'C=US,O=Internet Security Research Group,CN=ISRG Root X1' for certificate 'C=US,O=Let's Encrypt,CN=R3'

The "Certbot" here is just an example. The question relates to the ACME client used, whichever ACME client. In your case that seems to be Certes, so the question here really is: "The version of Certes".

Did you also look at the other (solved) threads with regard to this error and Certes? E.g. Certes.AcmeException: Can not find issuer 'C=US,O=Internet Security Research Group,CN=ISRG Root X1' for certificate 'C=US,O=Let's Encrypt,CN=R3' or Getting Error when trying to get a new certificate?

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