[Karellen]

Thanks for the reply. What scrapper should I use TVDB / TVDB Python or TVMAZE ? 

For tv shows? The default scraper is TMDB. You can use either TMDB or TVDB, but I think WatchedList relies on TVDB ID's. TMDB does have TVDB ID's, but whether they have been added for particular shows or episodes may not always be the case.
Maybe @schapplm can comment which would be better for TV shows.
For movies, IMDB ID's are needed so use TMDB.

Also do i need to delete all .nfo files before i do this ?

Yes, otherwise Kodi will keep using them instead of the scrapers.
Of course, when you rescrape your library, you are going to lose your current Watched status.
But I suppose it is a no-win situation. Rescrape and lose the status, Don't rescrape and WatchedList probably won't work, so you will end up losing the status sometime in the future anyway.

in medusa i take it i need to change the settings 

I don't know what Medusa is, and if the rest of your post relates to Medusa, then I have no idea.