Root Empty Phone Still Working With Latest Update, Please Help.

Apr 19, 2014
I have a problem.

Something went wrong while syncing to my nas. All folders are removed by the root. I look in Explorer, I can still see them in the internal memory. Phone still works with the latest ROM 1.6.28. If connect to the computer I get the message that the folder is empty.
Tried using the ROM Update again to install again, but than I come into the recovery mode. I can then choose from: reboot, wipe and reset installUpdate zip to one system, power off. The installed ROM is still in my download folder.

What should I do to get refilled my root directory with the correct folders? I'm not a real tweaker but more a follower of steps in full tutorials.

Thanks in advance.