Here is what I did, was downloading some tv shows with Transmission, using the windows client. When I open the torrent file in the windows client, depending what type it is, I will put in the corresponding path in the Transmission options. In this case it was /shares/video/tv - what I had forgotten was that the folder on the WBE was called /shares/video/TV.
So, after downloading a TV episode, I go check the folder in windows explorer and notice two of them, one is tv and the other is TV, both are identical as far as folders, contents etc. Without putting a lot of thought in it, I am thinking I must have accidentally created a copy of one somehow, and deleted the lowercase /shares/video/tv folder. Well, THAT was a mistake, as it promptly deleted 50 or so GB from both folders before I stopped it. Not catastrophic, just a PITA, since I can re download the seasons again that I had, but I notice now when I go in command line to the NAS drive I have the newly dowloaded and .part files in the /shares/tv folder, but not in the shares/TV folder! and I can only see them via putty command line, not in windows explorer.
I know a bit about linux, but am confused about what just happened here. Anyway, after my downloads are done I'll move the files into one safe folder, delete the lower case tv folder, then move them back to the TV folder.
Obviously windows was confused over the lower case upper case folder names, and I never thought it through when I tried to delete one of them, and lost a bunch of data because of this. I am confused though, on why I can't see any of the new files in the new tv folder in windows explorer.