Regarding deleted files and unremovable folders. I experiences the same issues like most of you. What I found is as follows:
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After I found that some some went missing I connected my HDD to Windows and ran chkdsk. It fixed some errors.
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Some video/audio files became folders! What was a file ‘movie.avi’ became a folder ‘movie.avi’.
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I could not delete the new folder ‘movie.avi’ though I could rename it.
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I also found that not only files that I watched were converted to folders but also files that I did not watch. I had thousands of files converted to folders.
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I connected the HDD to a PC with Ubuntu.
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In Ubuntu all ‘converted’ files-folders looked as files (not as folders like in Windows), and I could play/watch them.
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So in Ubuntu I copied all my movies from one folder to another and deleted old content.
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Now in Windows and WDTV I can see all ‘deleted/converted’ files again. Luckily I did not lose any file.
I will definitely downgrade to the previous version of firmware.