[MeMeMe]

I've had this problem a few times and it's usually easily fixed.
The trick is to disable the trakt addon before toggling the episodes to unwatched in xbmc, then removing them from the website (to be sure, remove them from both Collection and History), and only then re-enabling the trakt addon and running it.

If that isn't working, something else is up. This more thorough approach should work:

First, in xbmc trakt settings, switch off the tv settings EXCEPT clean shows from trakt. Make sure that is on.
Also, make sure trakt is set NOT to run after library update.
Now, in XBMC, make note of where you are in the TV show, and then remove it and all episodes from the library.
(alternatively, just remove the episodes that have been incorrectly marked watched)
Now run trakt manually, so it will delete the tv show and all episodes from the website.
Check the show is deleted from trakt - check both collection, and history, and remove them from both.
Now update xbmc library so it picks up the tv shows again. Check watched statuses are correct, and set them manually if not.
Now run trakt manually and check all is well.