@Aurquiel --- , Welcome to Microsoft Q&A, there are two methods to install the setup file in the ftp server.
However, we need to create the new FTP site in IIS regardless of using one of the two methods.
First, we could use clickonce to deploy the folder in the ftp directly.
Second, we could deploy the folder in the local and then upload its contents using an FTP client.
Hope my suggestions could help you.
Best regards,
Jack
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