The Fandango At Home Catalog tool will now clear your Watch list automatically.
First make sure you have it downloaded https://chromewebstore.google.com/detail/fandango-at-home-catalog/bnlpiockcfehbfbdcegahemgmjfkdopc
Then go to:
https://athome.fandango.com/content/movies/mylibrary
Click on Continue Watching here (you can't navigate directly)
Click on Clear Watchlist
Click Ok
Wait
If you have a large amount of movies on there you may have to do it more than once.
Once it's done you will see this:
Big thanks to Will for adding this!