What you quoted about naming:
Blockquote
/TV Shows/ShowName/Season 02/ShowName – s02e17 – Optional_Info.ext
This is only an example. The most important bit in the file name is the appropriate season and episode number notation s02e17 which in this example means Season 2 Episode 17 It does not matter if you use dashes, dots or just spaces.
refers to variations in naming such as ShowName – s02e17
or ShowName s02e17
or ShowName.s02e17
what matters is S00E00
Back to your original issue, I suspect that when you move data between locations, you are not Plex Dance ing them and are thus confusing Plex. Having a sub-par naming system does not help. I tested this by creating the same show in my library using dummy files. Guess what? it works just fine using the standard naming schema