Be sure to read https://yatse.tv/wiki/debug-yatse-kodi-remote to provide necessary logs and information.
Issue description:
I’ve removed many shows from Kodi and cleaned the library. They are not shown in Kodi.
When I sync yatse, the old shows are not removed from yatse. Multiple syncs don’t help either.
Logs:
Screenshots:
Additional information:
They are still in Kodi.
Uncheck Kodi option to hide empty show so you can really remove them
Thanks, that makes sense. Wouldn’t it be useful to have the same option in Yatse?
I don’t think ppl clean their tv shows such a way manually in Kodi, especially it since does not bother anything there.
People usually don’t clean them at all 
And Yatse is optimized for speed and low end devices, adding such option would slow down every thing for nearly no benefits.