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I just wanted to chime in that I have a similar issue that does not bother me too much. When I delete a file from my computer (from windows explorer), it does not get removed from the TV Series database. If I select that episode to play, I get a file not found error. In mediaportal, I have to bring up the context menu and choose to delete it from the database.

Is there an option somewhere I am missing?

Like the original poster, if I rename a file (or folder) of an episode already in the database, I will get two entries in the database.

thanks