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

Specifically, you need to ensure your python3-acme package is updated to 0.31.0-2, which has a fix backported from a future version, to address this specific issue.

apt update && apt install --only-upgrade python3-acme

(It is probably best if you upgrade all your packages, though).

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