No, exposing hidden files isn't fixed. I've deleted SKYBOX from my device, then reinstalled it from Oculus Store, and the problem still persists.
Steps which always reproduce this problem for me.
Add some video files to /SKYBOX/hide folder. Open SKYBOX (everything still may be okay), then enable "show hidden files" option. Then exit SKYBOX. Connect VR device to PC again, delete old video files from /SKYBOX/hide and upload other ones. Run SKYBOX again. All the new files are exposed. Switch to Directory view and then back to All files view again — the files disappear. But they all are shown right after SKYBOX start, and that's the problem.