ls -lr /etc/letsencrypt/live/
total 12
-rw-r--r-- 1 root root 740 Jul 28 03:35 README
drwxr-xr-x 2 root root 4096 Oct 30 14:26 mail.allanimals.info-0001
drwxr-xr-x 2 root root 4096 Jan 15 09:27 mail.allanimals.info
ls -lr /etc/letsencrypt/archive/
total 8
drwxr-xr-x 2 root root 4096 Jan 25 10:05 mail.allanimals.info-0001
drwxr-xr-x 2 root root 4096 Jan 25 10:04 mail.allanimals.info
Sorry, that failed to give me all I wanted...
Try:
ls -lr /etc/letsencrypt/live/*
AND
ls -lr /etc/letsencrypt/archive/*
Right there I see a problem.
These two have somewhat close dates:
drwxr-xr-x 2 root root 4096 Jan 15 09:27 mail.allanimals.info
drwxr-xr-x 2 root root 4096 Jan 25 10:04 mail.allanimals.info
These are nowhere near to each other:
drwxr-xr-x 2 root root 4096 Oct 30 14:26 mail.allanimals.info-0001
drwxr-xr-x 2 root root 4096 Jan 25 10:05 mail.allanimals.info-0001
Something went awry during that Jan 25 renewal.
ls -lr /etc/letsencrypt/live/*
-rw-r--r-- 1 root root 740 Jul 28 03:35 /etc/letsencrypt/live/README
/etc/letsencrypt/live/mail.allanimals.info-0001:
total 0
/etc/letsencrypt/live/mail.allanimals.info:
total 4
-rw-r--r-- 1 root root 692 Oct 30 14:28 README
lrwxrwxrwx 1 root root 52 Jan 15 09:27 privkey.pem -> ../../archive/mail.allanimals.info-0001/privkey1.pem
lrwxrwxrwx 1 root root 54 Jan 15 09:27 fullchain.pem -> ../../archive/mail.allanimals.info-0001/fullchain1.pem
lrwxrwxrwx 1 root root 50 Jan 15 09:27 chain.pem -> ../../archive/mail.allanimals.info-0001/chain1.pem
lrwxrwxrwx 1 root root 49 Jan 15 09:27 cert.pem -> ../../archive/mail.allanimals.info-0001/cert1.pem
ls -lr /etc/letsencrypt/archive/*
/etc/letsencrypt/archive/mail.allanimals.info-0001:
total 16
-rw------- 1 root root 1704 Oct 30 14:28 privkey1.pem
-rw-r--r-- 1 root root 3684 Oct 30 14:28 fullchain1.pem
-rw-r--r-- 1 root root 3765 Oct 30 14:48 chain1.pem
-rw-r--r-- 1 root root 1858 Oct 30 14:28 cert1.pem
/etc/letsencrypt/archive/mail.allanimals.info:
total 76
-rw------- 1 root root 1704 Oct 29 18:03 privkey4.pem
-rw------- 1 root root 1704 Sep 29 19:36 privkey3.pem
-rw------- 1 root root 1704 Jul 31 16:09 privkey2.pem
-rw------- 1 root root 1704 Jul 28 03:35 privkey1.pem
-rw-r--r-- 1 root root 5607 Oct 29 18:03 fullchain4.pem
-rw-r--r-- 1 root root 3680 Sep 29 19:36 fullchain3.pem
-rw-r--r-- 1 root root 3680 Jul 31 16:09 fullchain2.pem
-rw-r--r-- 1 root root 5608 Jul 28 03:35 fullchain1.pem
-rw-r--r-- 1 root root 5688 Oct 30 13:16 chain4.pem
-rw-r--r-- 1 root root 1826 Sep 29 19:36 chain3.pem
-rw-r--r-- 1 root root 3765 Jul 31 16:17 chain2.pem
-rw-r--r-- 1 root root 3750 Jul 28 03:35 chain1.pem
-rw-r--r-- 1 root root 1858 Oct 29 18:03 cert4.pem
-rw-r--r-- 1 root root 1854 Sep 29 19:36 cert3.pem
-rw-r--r-- 1 root root 1854 Jul 31 16:09 cert2.pem
-rw-r--r-- 1 root root 1858 Jul 28 03:35 cert1.pem
OK, the picture has been painted.
I see it clearly now:
/etc/letsencrypt/live/mail.allanimals.info-0001:
total 0
/etc/letsencrypt/live/mail.allanimals.info:
total 4
-rw-r--r-- 1 root root 692 Oct 30 14:28 README
lrwxrwxrwx 1 root root 52 Jan 15 09:27 privkey.pem -> ../../archive/mail.allanimals.info-0001/privkey1.pem
lrwxrwxrwx 1 root root 54 Jan 15 09:27 fullchain.pem -> ../../archive/mail.allanimals.info-0001/fullchain1.pem
lrwxrwxrwx 1 root root 50 Jan 15 09:27 chain.pem -> ../../archive/mail.allanimals.info-0001/chain1.pem
lrwxrwxrwx 1 root root 49 Jan 15 09:27 cert.pem -> ../../archive/mail.allanimals.info-0001/cert1.pem
The -0001 is empty.
And the original one points to the -0001 cert!
A good mess indeed.
OK. let's blow away the symlinks and recreate them.
The files seem to be in tact.
Ok. I'll make a copy of the directory first, just in case. Could you provide the command to redirect the sym links to where they should be pointing please.
Let's take the slow and steady path:
#1 unlink the incorrect links:
unlink /etc/letsencrypt/live/mail.allanimals.info/privkey.pem
unlink /etc/letsencrypt/live/mail.allanimals.info/fullchain.pem
unlink /etc/letsencrypt/live/mail.allanimals.info/chain.pem
unlink /etc/letsencrypt/live/mail.allanimals.info/cert.pem
Check they have been removed:
ls -l /etc/letsencrypt/live/mail.allanimals.info/
unlink /etc/letsencrypt/live/mail.allanimals.info/privkey.pem
unlink /etc/letsencrypt/live/mail.allanimals.info/fullchain.pem
unlink /etc/letsencrypt/live/mail.allanimals.info/chain.pem
unlink /etc/letsencrypt/live/mail.allanimals.info/cert.pem
ls -l /etc/letsencrypt/live/mail.allanimals.info/
total 4
-rw-r--r-- 1 root root 692 Oct 30 14:28 README
#2 relink the files:
cd /etc/letsencrypt/live/mail.allanimals.info/
ln -s ../../archive/mail.allanimals.info/privkey4.pem privkey.pem
ln -s ../../archive/mail.allanimals.info/fullchain4.pem fullchain.pem
ln -s ../../archive/mail.allanimals.info/chain4.pem chain.pem
ln -s ../../archive/mail.allanimals.info/cert4.pem cert.pem
cd /etc/letsencrypt/live/mail.allanimals.info-0001/
ln -s ../../archive/mail.allanimals.info-0001/privkey1.pem privkey.pem
ln -s ../../archive/mail.allanimals.info-0001/fullchain1.pem fullchain.pem
ln -s ../../archive/mail.allanimals.info-0001/chain1.pem chain.pem
ln -s ../../archive/mail.allanimals.info-0001/cert1.pem cert.pem
Then make sure they are working:
certbot certificates
#3 delete the cert you are not using/needing
certbot delete --cert-name mail.allanimals.info-0001
#4 renew the remaining cert [if needed]
certbot renew
cd /etc/letsencrypt/live/mail.allanimals.info/
/etc/letsencrypt/live/mail.allanimals.info# ln -s ../../archive/mail.allanimals.info/privkey4.pem privkey.pem
/etc/letsencrypt/live/mail.allanimals.info# ln -s ../../archive/mail.allanimals.info/fullchain4.pem fullchain.pem
/etc/letsencrypt/live/mail.allanimals.info# ln -s ../../archive/mail.allanimals.info/chain4.pem chain.pem
/etc/letsencrypt/live/mail.allanimals.info# ln -s ../../archive/mail.allanimals.info/cert4.pem cert.pem
/etc/letsencrypt/live/mail.allanimals.info# cd /etc/letsencrypt/live/mail.allanimals.info-0001/
/etc/letsencrypt/live/mail.allanimals.info-0001# ln -s ../../archive/mail.allanimals.info-0001/privkey1.pem privkey.pem
/etc/letsencrypt/live/mail.allanimals.info-0001# ln -s ../../archive/mail.allanimals.info-0001/fullchain1.pem fullchain.pem
/etc/letsencrypt/live/mail.allanimals.info-0001# ln -s ../../archive/mail.allanimals.info-0001/chain1.pem chain.pem
/etc/letsencrypt/live/mail.allanimals.info-0001# ln -s ../../archive/mail.allanimals.info-0001/cert1.pem cert.pem/etc/letsencrypt/live/mail.allanimals.info-0001# certbot certificates
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Renewal configuration file /etc/letsencrypt/renewal/mail.allanimals.info-0001.conf produced an unexpected error: fullchain does not match cert + chain for mail.allanimals.info-0001!. Skipping.
Renewal configuration file /etc/letsencrypt/renewal/mail.allanimals.info.conf produced an unexpected error: fullchain does not match cert + chain for mail.allanimals.info!. Skipping.
The following renewal configurations were invalid:
/etc/letsencrypt/renewal/mail.allanimals.info-0001.conf
/etc/letsencrypt/renewal/mail.allanimals.info.conf
How does this happen?!?!?!
One at a time:
ls -l /etc/letsencrypt/live/mail.allanimals.info/
I have no idea! 
/etc/letsencrypt/live/mail.allanimals.info-0001# ls -l /etc/letsencrypt/live/mail.allanimals.info/
total 4
lrwxrwxrwx 1 root root 44 Jan 26 08:56 cert.pem -> ../../archive/mail.allanimals.info/cert4.pem
lrwxrwxrwx 1 root root 45 Jan 26 08:56 chain.pem -> ../../archive/mail.allanimals.info/chain4.pem
lrwxrwxrwx 1 root root 49 Jan 26 08:56 fullchain.pem -> ../../archive/mail.allanimals.info/fullchain4.pem
lrwxrwxrwx 1 root root 47 Jan 26 08:56 privkey.pem -> ../../archive/mail.allanimals.info/privkey4.pem
-rw-r--r-- 1 root root 692 Oct 30 14:28 README
I see a problem we missed before:
That chain is from the following day!
cat /etc/letsencrypt/renewal/mail.allanimals.info.conf
version = 1.32.2
archive_dir = /etc/letsencrypt/archive/mail.allanimals.info
cert = /etc/letsencrypt/live/mail.allanimals.info/cert.pem
privkey = /etc/letsencrypt/live/mail.allanimals.info/privkey.pem
chain = /etc/letsencrypt/live/mail.allanimals.info/chain.pem
fullchain = /etc/letsencrypt/live/mail.allanimals.info/fullchain.pem
[renewalparams]
account = 994651a718b257d6f21dd3959b6cc9d6
authenticator = standalone
server = https://acme-v02.api.letsencrypt.org/directory
key_type = rsa
preferred_chain = ISRG Root X1
Time for the surgical gloves the come on...
cat /etc/letsencrypt/archive/mail.allanimals.info/fullchain4.pem
cat /etc/letsencrypt/archive/mail.allanimals.info/fullchain4.pem
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----