LetsEncrypt problems since upgrade to 3.2.8p1

Since upgrading from 3.2.7p1 to 3.2.8p1 (without any reported errors or warnings - running Ubuntu 20.04.4 LTS) we have been experiencing LetsEncrypt problems. We first started getting SSL errors on one of our email accounts and found these errors in the logs:

Code:

postfix-script (total: 5)
         1   symlink leaves directory: /etc/postfix/./smtpd.key
         1   symlink leaves directory: /etc/postfix/./smtpd.cert-20210327132...
         1   symlink leaves directory: /etc/postfix/./smtpd.cert
         1   symlink leaves directory: /etc/postfix/./makedefs.out
         1   symlink leaves directory: /etc/postfix/./smtpd.key-202103271327...

and in the LetsEncrypt logs:

Code:

2022-05-11 16:31:59,181:DEBUG:certbot.storage:Should renew, less than 30 days before certificate expiry 2021-04-14 10:53:44 UTC.
2022-05-11 16:31:59,181:INFO:certbot.renewal:Cert is due for renewal, auto-renewing...
2022-05-11 16:31:59,181:DEBUG:certbot.plugins.selection:Requested authenticator manual and installer None
2022-05-11 16:31:59,182:DEBUG:certbot.plugins.disco:Other error:(PluginEntryPoint#manual): An authentication script must be provided with --manual-auth-hook when using the manual plugin non-interactively.
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/certbot/plugins/disco.py", line 130, in prepare
    self._initialized.prepare()
  File "/usr/lib/python3/dist-packages/certbot/plugins/manual.py", line 87, in prepare
    raise errors.PluginError(
certbot.errors.PluginError: An authentication script must be provided with --manual-auth-hook when using the manual plugin non-interactively.
2022-05-11 16:31:59,184:DEBUG:certbot.plugins.selection:No candidate plugin
2022-05-11 16:31:59,184:DEBUG:certbot.plugins.selection:Selected authenticator None and installer None
2022-05-11 16:31:59,185:INFO:certbot.main:Could not choose appropriate plugin: The manual plugin is not working; there may be problems with your existing configuration.
The error was: PluginError('An authentication script must be provided with --manual-auth-hook when using the manual plugin non-interactively.')
2022-05-11 16:31:59,185:WARNING:certbot.renewal:Attempting to renew cert (emstaffs.uk) from /etc/letsencrypt/renewal/emstaffs.uk.conf produced an unexpected error: The manual plugin is not working; there may be problems with your existing configuration.
The error was: PluginError('An authentication script must be provided with --manual-auth-hook when using the manual plugin non-interactively.'). Skipping.
2022-05-11 16:31:59,190:DEBUG:certbot.renewal:Traceback was:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/certbot/renewal.py", line 462, in handle_renewal_request
    main.renew_cert(lineage_config, plugins, renewal_candidate)
  File "/usr/lib/python3/dist-packages/certbot/main.py", line 1202, in renew_cert
    installer, auth = plug_sel.choose_configurator_plugins(config, plugins, "certonly")
  File "/usr/lib/python3/dist-packages/certbot/plugins/selection.py", line 235, in choose_configurator_plugins
    diagnose_configurator_problem("authenticator", req_auth, plugins)
  File "/usr/lib/python3/dist-packages/certbot/plugins/selection.py", line 339, in diagnose_configurator_problem
    raise errors.PluginSelectionError(msg)
certbot.errors.PluginSelectionError: The manual plugin is not working; there may be problems with your existing configuration.
The error was: PluginError('An authentication script must be provided with --manual-auth-hook when using the manual plugin non-interactively.')
2022-05-11 16:31:59,204:INFO:certbot.renewal:Cert not yet due for renewal
2022-05-11 16:31:59,205:DEBUG:certbot.plugins.selection:Requested authenticator webroot and installer None
2022-05-11 16:31:59,206:WARNING:certbot.renewal:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/certbot/renewal.py", line 65, in _reconstitute
    renewal_candidate = storage.RenewableCert(full_path, config)
  File "/usr/lib/python3/dist-packages/certbot/storage.py", line 444, in __init__
    raise errors.CertStorageError(
certbot.errors.CertStorageError: renewal config file {} is missing a required file reference
2022-05-11 16:31:59,208:WARNING:certbot.renewal:Renewal configuration file /etc/letsencrypt/renewal/server1.16bit.co.conf is broken. Skipping.
2022-05-11 16:31:59,208:DEBUG:certbot.renewal:Traceback was:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/certbot/renewal.py", line 65, in _reconstitute
    renewal_candidate = storage.RenewableCert(full_path, config)
  File "/usr/lib/python3/dist-packages/certbot/storage.py", line 444, in __init__
    raise errors.CertStorageError(
certbot.errors.CertStorageError: renewal config file {} is missing a required file reference
2022-05-11 16:31:59,227:INFO:certbot.renewal:Cert not yet due for renewal
2022-05-11 16:31:59,228:DEBUG:certbot.plugins.selection:Requested authenticator webroot and installer None
2022-05-11 16:31:59,244:INFO:certbot.renewal:Cert not yet due for renewal
2022-05-11 16:31:59,245:DEBUG:certbot.plugins.selection:Requested authenticator webroot and installer None
2022-05-11 16:31:59,245:ERROR:certbot.renewal:All renewal attempts failed. The following certs could not be renewed:
2022-05-11 16:31:59,245:ERROR:certbot.renewal:  /etc/letsencrypt/live/16bit.co/fullchain.pem (failure)
  /etc/letsencrypt/live/aretheassholesstillincharge.com/fullchain.pem (failure)
  /etc/letsencrypt/live/emstaffs.uk/fullchain.pem (failure)
2022-05-11 16:31:59,246:DEBUG:certbot.log:Exiting abnormally:
Traceback (most recent call last):
  File "/usr/bin/certbot", line 11, in <module>
    load_entry_point('certbot==0.40.0', 'console_scripts', 'certbot')()
  File "/usr/lib/python3/dist-packages/certbot/main.py", line 1382, in main
    return config.func(config, plugins)
  File "/usr/lib/python3/dist-packages/certbot/main.py", line 1287, in renew
    renewal.handle_renewal_request(config)
  File "/usr/lib/python3/dist-packages/certbot/renewal.py", line 486, in handle_renewal_request
    raise errors.Error("{0} renew failure(s), {1} parse failure(s)".format(
certbot.errors.Error: 3 renew failure(s), 1 parse failure(s)

Any ideas as to what could have gone wrong and/or how to fix. I'm reluctant to mess around with Certbot without understanding what caused the problem and I don't want to screw up ISPConfig.
Many thanks.

 

OK, thanks for the suggestions till, I'll take a look.