I was in your shoes. At one point I was using the <show> - [SSxEE] - <Title> format, I had lost 1/3 of my library before I caught what was happening.
When you are moving around and renaming files make sure you Plex Dance them otherwise you may not get the results you want.
should add anything video it finds. Wrong, Plex shows anything it can recognize as a valid for the library type defined, anything it doesnt understand it ignores.
