Let's Encrypt certificates being regenerated instead of renewed?

Summary

Let's Encrypt certificates seems to be regenerated instead of renewed

Steps to reproduce

Omnibus installation on an https domain (no longer using the "old" way)
Wait for near-expiry of first certificate
Receive an email indicating the certificate is expiring, even though it was renewed already at this point.

Example Project

N/A

What is the current bug behavior?

Let's encrypt certificate seems to be regenerated instead of renewed upon expiry, causing Let's encrypt to send reminder emails (and likely hitting Let's Encrypt limits more quickly)

What is the expected correct behavior?

Let's Encrypt certificate should be renewed instead of regenerated

Relevant logs and/or screenshots

Output of checks

Results of GitLab environment info

Expand for output related to GitLab environment info

System information System: Proxy: no Current User: git Using RVM: no Ruby Version: 2.4.4p296 Gem Version: 2.7.6 Bundler Version:1.16.2 Rake Version: 12.3.1 Redis Version: 3.2.11 Git Version: 2.18.0 Sidekiq Version:5.1.3 Go Version: unknown

GitLab information Version: 11.2.3-ee Revision: aadca99 Directory: /opt/gitlab/embedded/service/gitlab-rails DB Adapter: postgresql DB Version: 9.6.8 URL: https://gitlab.minit-europe.com HTTP Clone URL: https://gitlab.minit-europe.com/some-group/some-project.git SSH Clone URL: git@gitlab.minit-europe.com:some-group/some-project.git Elasticsearch: no Geo: no Using LDAP: yes Using Omniauth: no

GitLab Shell Version: 8.1.1 Repository storage paths:

default: /var/opt/gitlab/git-data/repositories Hooks: /opt/gitlab/embedded/service/gitlab-shell/hooks Git: /opt/gitlab/embedded/bin/git

Results of GitLab application Check

Expand for output related to the GitLab application check


Checking GitLab Shell ...

GitLab Shell version >= 8.1.1 ? ... OK (8.1.1)
Repo base directory exists?
default... yes
Repo storage directories are symlinks?
default... no
Repo paths owned by git:root, or git:git?
default... yes
Repo paths access is drwxrws---?
default... yes
hooks directories in repos are links: ...
3/1 ... ok
3/2 ... ok
3/3 ... ok
3/4 ... ok
3/5 ... ok
3/6 ... ok
3/7 ... repository is empty
3/9 ... repository is empty
3/10 ... ok
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Check GitLab API access: OK
Redis available via internal API: OK

Access to /var/opt/gitlab/.ssh/authorized_keys: OK
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Sidekiq ...

Running? ... yes
Number of Sidekiq processes ... 1

Checking Sidekiq ... Finished

Checking Reply by email ...

IMAP server credentials are correct? ... yes
Init.d configured correctly? ... skipped
MailRoom running? ... skipped

Checking Reply by email ... Finished

Checking LDAP ...

Server: ldapmain
LDAP authentication... Success
LDAP users with access to your GitLab server (only showing the first 100 results)
        ==redacted==

Checking LDAP ... Finished

Checking GitLab ...

Git configured correctly? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config up to date? ... yes
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory exists? ... yes
Uploads directory has correct permissions? ... yes
Uploads directory tmp has correct permissions? ... yes
Init script exists? ... skipped (omnibus-gitlab has no init script)
Init script up-to-date? ... skipped (omnibus-gitlab has no init script)
Projects have namespace: ...
3/1 ... yes
3/2 ... yes
3/3 ... yes
3/4 ... yes
3/5 ... yes
3/6 ... yes
3/7 ... yes
3/9 ... yes
3/10 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.3.5 ? ... yes (2.4.4)
Git version >= 2.9.5 ? ... yes (2.18.0)
Git user has default SSH configuration? ... yes
Active users: ... 3
Elasticsearch version 5.1 - 5.5? ... skipped (elasticsearch is disabled)

Checking GitLab ... Finished

Possible fixes

(If you can, link to the line of code that might be responsible for the problem)