I appreciate I am resurrecting an old post, but did you resolve this?
I am struggling with the same issue. The nextcloud Android App (version 3.26.0) doesn’t list any of the files on my server.
With the search tool I can find and open documents that I know exist, however it prevents me from moving or copying files because I cannot navigate the filetree.
The servers web interface works fine and lists the files.
since some weeks, on the Android App I see a message “server unavalable” but I always had access to my files, but a few days ago I disconnect and reconnect the server on the App, and now, I see none of my files.
But I still can find my files using the search tool.
That should give a clearer idea of what is going on.
It also would be informative to check your server-side logs (NC logs, web server logs) to see what is going on around the time you open, login, and refresh your All Files list in the client app.