[cookem]

I am having an issue when I go into my tv shows in library view where i see shows that I long removed from the library. If I go into a show with episodes and come back out then those old deleted shows disappear. I tried the kodi default skin and did not see this issue.

That is strange but can not be skin related. The library sections are completely controlled by Kodi itself, not the skin.
The skin only displays whatever Kodi is providing.

Maybe you've configured your homescreen shortcut to not point at the TV shows library but the file location instead or something ?

seems like a kodi bug then that it is not following the advancedsettings.xml to hide empty series (i have this set to true)

<hideemptyseries>false</hideemptyseries> <!-- set to "true" to hide empty series in the video library and prevent empty series from being removed during a library cleanup. -->