No offense, but ...
Really!!!???!!!! you are wanting me/we to sort through you logs looking for the date you did the upgrade? Wow! That's really asking for the 'extra mile' ... for free too! :\
As server admin or one who has that access level and as admin of the your moodle with issues, isn't that something you should do/learn?
Search for 'Jul 03' ...
First entry for Jul 03:
[Wed Jul 03 00:00:01.900190 2019] [mpm_prefork:notice] [pid 13258] AH00171: Graceful restart requested, doing restart
[Wed Jul 03 00:00:01.955997 2019] [mpm_prefork:notice] [pid 13258] AH00163: Apache/2.4.33 (Linux/SUSE) OpenSSL/1.1.0i-fips mod_jk/1.2.43 PHP/7.2.5 configured -- resuming normal operations
Others that you need to check into:
[Wed Jul 03 00:38:00.858578 2019] [core:notice] [pid 13472] AH00094: Command line: '/usr/sbin/httpd-prefork -D SYSCONFIG -D SSL -C PidFile /var/run/httpd.pid -C Include /etc/apache2/sysconfig.d//loadmodule.conf -C Include /etc/apache2/sysconfig.d//global.conf -f /etc/apache2/httpd.conf -c Include /etc/apache2/sysconfig.d//include.conf -D SYSTEMD -D FOREGROUND'
libpng warning: iCCP: known incorrect sRGB profile
libpng warning might be nothing but aren't you curious?
and I do see a few config files that have // in front? ... which I assume load anyway, even though I would think they should look like:
with single / rather than doubles //.
Here's the first concerning LDAP user which you kinda explained:
[Wed Jul 03 00:39:10.827087 2019] [php7:notice] [pid 13483] [client 10.0.26.101:46190] [ENROL LDAP] Server: 'ldap://uranos.paes.eit.htwk-leipzig.de', Connection: 'Resource id #16', STARTTLS failed.\n, referer: https://moodle.paes.eit.htwk-leipzig.de/moodle/login/index.php
STARTTLS is certificate stuff (failed) and appears the user ID is 16 in mdl_user table?
So are all your admin level folks in your Moodle have LDAP as auth or manual?
Last line for Jul 03 and first line for Jul 04
[Wed Jul 03 22:54:32.937747 2019] [php7:notice] [pid 15588] [client 10.0.26.101:47538] [ENROL LDAP] Server: 'ldap://uranos.paes.eit.htwk-leipzig.de', Connection: 'Resource id #33', STARTTLS failed.\n, referer: https://moodle.paes.eit.htwk-leipzig.de/moodle/login/index.php
[Thu Jul 04 07:25:58.234511 2019] [php7:notice] [pid 14922] [client 10.0.26.101:47566] [ENROL LDAP] Server: 'ldap://uranos.paes.eit.htwk-leipzig.de', Connection: 'Resource id #15', STARTTLS failed.\n, referer: https://moodle.paes.eit.htwk-leipzig.de/moodle/login/index.php
In your ssl_request_log-20190703 log ... cannot find 03/Jul in entire log file!!!!
First line: [28/Jun/2019
*** last line ***
[02/Jul/2019:23:52:41 +0200] 10.0.26.101 TLSv1.2 ECDHE-RSA-AES256-GCM-SHA384 "POST /moodle/lib/ajax/service.php?sesskey=AX1iUV0DaP&info=core_fetch_notifications HTTP/1.1" 27 "https://moodle.paes.eit.htwk-leipzig.de/moodle/login/index.php" "Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Firefox/60.0"
Have already done way over what should be expected - free support. Suggest you review and search logs and IF you see something that looks like an error ... investigate!
Google is your friend!
I'll do below to the best of my ability ... as a community member ... even if I don't work for moodle.net nor admin that server. So can't say what their policies are in how strict registering a server is with them.
1.) Do I right understand, that I can truncated the mdl_registration_hubs table? (I would of course copy the db before ! )?
I said I did a test on a server that doesn't have the issue you have by truncating the table then renewed the registration without error.
And yes, would always be a good idea to make a backup of the database IF manipulating directly. That's SOP!
2.) Are the admin user credentials locally stored in the db?
If accounts are manual, which at least one admin level user should be (ie, no other auth like LDAP), then yes ... everything ... including password ... in the DB server pointed to ... localhost?
User ID's ... 1 is guest user ... 2 was/is the first user that installed them moodle.
mysql> select * from mdl_user where id = 2;
Password is not in clear text but has been hashed, etc.
You can change, however, using admin/cli/reset_password.php for maual accounts only.
3.) What does it mean: ..... You can also manually update your registration at any time.
That bit of info was seen after registering and renewing registration with Moodle.net. I assume it means one can, from the form, update registration info at any time ... but I've not found any CLI script that does that.