Missing directories and files after updating WD TV Live Firmware

I have lost directories and files on my “My Book World Edition NAS” after updating firmware on my WD TV Live. I had both connected to the LAN when updating the firmware. I upgraded from 1.04.31 to 1.06.15. Is there any way of getting my directories and files back?

Wait, you updated the firmware on the WD TV and now you are missing files in your NAS? This is almost impossible, have you try resetting both devices?

Yes thats correct… Both were connected on the same LAN. In the system log for  my NAS it said lost path to Shared Video, Shared Music Shared Music. I also lost other personal directories. I also noticed  5 hidden files on the root directory of the NAS which I never seen before. .AppleDB, .AppleDesktop, .AppleDouble, wd_tv and _VJDGT~V…

Yes I have reset both devices. I also rolled back the firmware on the WD TV Live and updated the firmware on the NAS.