Restore full chain.pem

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update_symlinks won't restore a deleted symlink, unfortunately.

First, take a backup of /etc/letsencrypt:

sudo tar cf /root/letsencrypt.tar /etc/letsencrypt

Then you can try run this to fix them up (make sure to substitute CERTIFICATE_NAME's value):

export CERTIFICATE_NAME=example.com
sudo bash -E <<EOF
cd "/etc/letsencrypt/live/${CERTIFICATE_NAME}" && \
ln -sf $(sudo find ../../archive/${CERTIFICATE_NAME}/ -name "fullchain*.pem" | sort | tail -1) fullchain.pem && \
ln -sf $(sudo find ../../archive/${CERTIFICATE_NAME}/ -name "privkey*.pem" | sort | tail -1) privkey.pem
ln -sf $(sudo find ../../archive/${CERTIFICATE_NAME}/ -name "chain*.pem" | sort | tail -1) chain.pem
ln -sf $(sudo find ../../archive/${CERTIFICATE_NAME}/ -name "cert*.pem" | sort | tail -1) cert.pem
EOF
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