If you can provide some screenshots or a video, combined with a directory tree listing that would be great. You might be best raising a ticket to post these. Make sure you blank anything out which is personal. Hopefully that will give me some further clues as to what is going wrong here.
My init.org looks like this right now:
* enable sub-folders #+begin_src scheme (set! sync-subfolders #t) #+end_src
The problem remains the same. I reinstall beorg, link the folder to Working Copy and at first everything is found. A moment later some of my files aren't found anymore.
When I open the files tab the first level of subfolders is shown. After tapping on a folder and switching to the sublevel some (not all!) subfolders are shown although I can find them through search and they're shown in the search results.
The init.org uses headlines to organise the content. For example
* Enable sub-folders #+begin_src scheme (set! sync-subfolders #t) #+end_src
Make sure you have the Scheme underneath a headline. If this is still not working attach your complete init.org file and I'll take a look.
Line 2 should be indented. Somehow this was messed up.
Bernhard Römer