Could you please advice me on how to retrieve the master site back to use it's own configuration file?

Should I change the php script, delete the symbolic links from multisites files?

My next step would be to delete the joomla site and restore an older Akeeba backup, from before this problem appeared.

Do I really need to delete everything and restore a previous Joomla in order to fix this?

Isn't there any other way, edwin2win?

Finally, by comparing the multisite php files and editing accordingly I managed to retrieve the master configuration file.

I am now able to uninstall MultiSite and forget about it. Maybe I will use it on a cPanel, but on Plesk it needs tremendous work + a good developer. For beginner developers it is too hard to control.

I'll just go back to common Joomla installations for now.

1) When using Plesk, if you have a recent version, you need to use the Plesk subscription functinoalities to manage correctly the owner of files and folders.
In this case, this avoid the need to use the Joomla FTP Layer

2) When the Joomla FTP Layer is used and when you don't put any FTP Root directory then this is the home directory of your FTP account.

When creating a slave site with the FTP Layer enabled, you need to provide at the slave site creation, the correct new FTP Root path for the slave site that is relative to the master path location. So you may have to use ../ to go up from the master FTP root directory.

3) Symbolic links are only used for the slave site.
The master website does not use Symbolic Link.

if you want to discard the patches installed in JMS, you can always unzip a joomla over the current installation.
You will have to remove the "/installation" directory to login.

If you just want temporarly disable JMS processing, you can also do that by addition a file or a folder in /includes/multisites_disable.php

Thank you for the clarifications.