Shows where exactly?
There's long been a setting accessible via the "Sharing" menu option that hides a file from the Open Remote dialog. This has to be set before you upload the file to the server.
On our old server from a workstation it would require us to login first then only show the files the user has rights too whereas currently it shows all files and then requests login. I put all the files in a folder but when I connect it shows all files on the server
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I'm not sure that you can specify only a particular subfolder to show with FileMaker Server.
You can enable the option "List only the databases each user is authorized to access" and this will require the user to authenticate when using Open Remote to only see folders their account exists in. This is in the FileMaker Server Database -> Security settings.
In the Solutions themselves, you can go to File -> Sharing -> Share with FileMaker Clients and enable to the box "Don't display in Launch Center" to hide the file from showing up in the Launch Center.
It would seem as has just been posted, that "List only the databases each user is authorized to access" is the setting that you need to investigate on your new server.