Attempting to renew cert from /etc/letsencrypt/renewal/domain.conf produced an unexpected error: urn:ietf:params:acme:error:malformed :: The request message was malformed :: Method not allowed. Skipping

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Correct; it is NOT certbot that needs to be updated.
[that --version will remain unchanged]
It is only the python3-acme that needs to be updated.

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