Problem with letsencrypt after migration.

I got problem with letsencrypt certificates.
1st i have noticed, that my dovecot is using wrong cert. Then i checked if links are directing into correct folder inside letsencrypt /etc/. And it did. I didn't want to play with searching where and why things happen like that, so i go directly into ispc to see how about main server domain, and Letsencrypt was not checked (it was migrated with migration tool, and should be checked on).
I checked it and save, but inside letsencrypt log there is only:
MissingCommandlineFlag: Missing command line flag or config entry for this setting:
Please choose an account
Choices: ['server.domain.pl@2016-03-08T18:45:14Z (66c0)', 'server2.domain.pl@2019-01-24T14:37:13Z (c5e9)'].
I do not really know what to do next ;s
Update:
I removed second domain, but it still asking for it in the end (i removed ssl first, and then delete whole website in ispc), here is the full log;

Code:

2019-02-03 12:40:03,065:DEBUG:certbot.main:certbot version: 0.30.0
2019-02-03 12:40:03,065:DEBUG:certbot.main:Arguments: ['-n', '--text', '--agree-tos', '--expand', '--authenticator', 'webroot', '--server', 'https://acme-v02
.api.letsencrypt.org/directory', '--rsa-key-size', '4096', '--email', '[email protected]', '--domains', 'server.domain.pl', '--webroot-path', '/usr/loc
al/ispconfig/interface/acme']
2019-02-03 12:40:03,065:DEBUG:certbot.main:Discovered plugins: PluginsRegistry(PluginEntryPoint#apache,PluginEntryPoint#manual,PluginEntryPoint#nginx,PluginE
ntryPoint#null,PluginEntryPoint#standalone,PluginEntryPoint#webroot)
2019-02-03 12:40:03,074:WARNING:certbot.cli:You are running with an old copy of letsencrypt-auto that does not receive updates, and is less reliable than mor
e recent versions. The letsencrypt client has also been renamed to Certbot. We recommend upgrading to the latest certbot-auto script, or using native OS pack
ages.
2019-02-03 12:40:03,074:DEBUG:certbot.cli:Deprecation warning circumstances: /opt/eff.org/certbot/venv/bin/certbot / {'LANG': 'en_US.UTF-8', 'SHELL': '/bin/s
h', 'XDG_RUNTIME_DIR': '/run/user/0', 'LOADEDMODULES': '', 'HOME': '/root', 'HOSTNAME': 'server.domain.pl', 'HISTSIZE': '1000', 'HISTCONTROL': 'ignoredups', 'S
HLVL': '3', 'PWD': '/usr/local/ispconfig/server', 'LOGNAME': 'root', 'USER': 'root', 'MAIL': '/var/spool/mail/root', 'PATH': '/sbin:/usr/sbin:/bin:/usr/bin:/
usr/local/sbin:/usr/local/bin:/usr/X11R6/bin', 'LESSOPEN': '||/usr/bin/lesspipe.sh %s', 'XDG_SESSION_ID': '9927', 'MODULESHOME': '/usr/share/Modules', '_': '
/opt/eff.org/certbot/venv/bin/certbot', 'MODULEPATH': '/usr/share/Modules/modulefiles:/etc/modulefiles'}
2019-02-03 12:40:03,080:DEBUG:certbot.log:Root logging level set at 20
2019-02-03 12:40:03,080:INFO:certbot.log:Saving debug log to /var/log/letsencrypt/letsencrypt.log
2019-02-03 12:40:03,080:DEBUG:certbot.plugins.selection:Requested authenticator webroot and installer None
2019-02-03 12:40:03,085:DEBUG:certbot.plugins.selection:Single candidate plugin: * webroot
Description: Place files in webroot directory
Interfaces: IAuthenticator, IPlugin
Entry point: webroot = certbot.plugins.webroot:Authenticator
Initialized: <certbot.plugins.webroot.Authenticator object at 0x7f78f3994e90>
Prep: True
2019-02-03 12:40:03,085:DEBUG:certbot.plugins.selection:Selected authenticator <certbot.plugins.webroot.Authenticator object at 0x7f78f3994e90> and installer
 None
2019-02-03 12:40:03,086:INFO:certbot.plugins.selection:Plugins selected: Authenticator webroot, Installer None
2019-02-03 12:40:03,093:DEBUG:certbot.log:Exiting abnormally:
Traceback (most recent call last):
  File "/opt/eff.org/certbot/venv/bin/certbot", line 11, in <module>
    sys.exit(main())
  File "/opt/eff.org/certbot/venv/lib/python2.7/site-packages/certbot/main.py", line 1364, in main
    return config.func(config, plugins)
  File "/opt/eff.org/certbot/venv/lib/python2.7/site-packages/certbot/main.py", line 1233, in certonly
    le_client = _init_le_client(config, auth, installer)
  File "/opt/eff.org/certbot/venv/lib/python2.7/site-packages/certbot/main.py", line 604, in _init_le_client
    acc, acme = _determine_account(config)
  File "/opt/eff.org/certbot/venv/lib/python2.7/site-packages/certbot/main.py", line 513, in _determine_account
    acc = display_ops.choose_account(accounts)
  File "/opt/eff.org/certbot/venv/lib/python2.7/site-packages/certbot/display/ops.py", line 86, in choose_account
    "Please choose an account", labels, force_interactive=True)
  File "/opt/eff.org/certbot/venv/lib/python2.7/site-packages/certbot/display/util.py", line 507, in menu
    self._interaction_fail(message, cli_flag, "Choices: " + repr(choices))
  File "/opt/eff.org/certbot/venv/lib/python2.7/site-packages/certbot/display/util.py", line 469, in _interaction_fail
    raise errors.MissingCommandlineFlag(msg)
MissingCommandlineFlag: Missing command line flag or config entry for this setting:
Please choose an account
Choices: ['server.domain.pl@2016-03-08T18:45:14Z (66c0)', 'server.domain2.pl@2019-01-24T14:37:13Z (c5e9)']

Update nr 2
Ok, what i did was the more testing. First, i was thinking that my dovecot cert is wrong, because outlook 2010 told me so. but it looks, like Outlook 2010 is using HTTPS certificate, because checking on other clients, and using openssl is showing correct values.

# cat /etc/dovecot.conf
listen = *,[::]
protocols = imap pop3
auth_mechanisms = plain login
disable_plaintext_auth = no
log_timestamp = "%Y-%m-%d %H:%M:%S "
mail_privileged_group = vmail
ssl_cert = </etc/postfix/smtpd.cert
ssl_key = </etc/postfix/smtpd.key
ssl_protocols = !SSLv3

Now from different box in the internet:

# openssl x509 -in /etc/postfix/smtpd.cert -text -noout
Certificate:
Data:
Version: 3 (0x2)
Serial Number:
xxxxxxxxxxxxxxxxxxxxxxxxx
Signature Algorithm: sha256WithRSAEncryption
Issuer: C=US, O=Let's Encrypt, CN=Let's Encrypt Authority X3
Validity
Not Before: Dec 4 02:00:57 2018 GMT
Not After : Mar 4 02:00:57 2019 GMT
Subject: CN=server.domain.pl
Subject Public Key Info:
Public Key Algorithm: rsaEncryption
Public-Key: (2048 bit)

Domain is correct!
# openssl s_client -connect server.domain.pl:993 -crlf
CONNECTED(00000003)
depth=2 O = Digital Signature Trust Co., CN = DST Root CA X3
verify return:1
depth=1 C = US, O = Let's Encrypt, CN = Let's Encrypt Authority X3
verify return:1
depth=0 CN = server.domain.pl
verify return:1

Domain here is also correct! Same for POP3, SMTP, and SMTP with STARTTLS.

So the only problem now, is on https, it use wrong certificate for the website, that use domain same as server do for ispc panel.

 

This is what i did, and it worked. Thank You.