We have experienced an issue with the desktop Filr client (and not the mobile or web app) where user files and folders are not showing up below the top level of their home directories.

If you look in their mapped drives in Windows, in the web app, or on a mobile app, all of their files will be there. On the desktop client, you can go into their top level 'My Files' folder and see everything that they store in their home folders but if you go into a folder from there, there will be nothing in that folder. If they were to go to the web client and drill down to that folder or lower, the desktop client will synchronize that folder alone on its next sync but none of the other contents of that folder.

I'm not seeing any settings we can change to force Filr to do a full file and folder synchronization of folders below the top level. Asking people to visit all of their individual folders on the web client before they use the desktop client is not a solution.