If you don't have the other slave site displayed in the JMS Tools, this probably mean that you have created an infinite loop in the webstie dependencies.
The loop can be created when you defined a website that is build on its children.
How do you want create a website based on a children if you are not yet born.
Check the template used in each slave site to identify the loop and remove it.
When the Tool detect the loop, it stop to read the definition of the website as it does not know how to display them.
If you have decided to create a copy of the administrator directory, this may cause you problem of consistencies. JMS Multisites does not contain any Syncrhonisation mechanism that would update all the files and folders between such separated directories.
You have to use Symbolic Link to ensure that the administrator directory is identical.
conf_multisites.php are internal JMS Multisites file that store the slave site definitions.
This does not correpond to the joomla configuration.php file.
When using the Joomla FTP Layer, you have to ensure that the FTP root path is correctly defined to reflect the deployed directory. If you don't manage it correctly, you could replace your master website with a slave site.
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