If you noticed that you're unable to see files and folders in the Desktop App / Egnyte Drive that exist in the cloud, it's likely you're using an unsupported version of the app.
Since February of this year, we stopped supporting version 1.x of the Desktop App / Egnyte Drive for Windows.
To resolve the problem of missing folders and / or files, please upgrade to the latest version of the Desktop App for Windows. You can download the latest version of the Desktop App here and directly upgrade any 1.x version of Egnyte Drive using the installer.
If you continue seeing that folders and / or files are missing after upgrading, please contact support with details of the folders where you're not seeing content that you're expecting to see.