How do I remove a game already removed from Steam from my Wishlist?

Generally synching with SG helps.

The Augmented Steam extension allows you to remove games directly from your wishlist page, I imagine it would work on games removed from the Steam store.

It's a bug with Steam. If you've wishlisted something and then it's removed - it stays on your wishlist.
Try the tips here.

Try this https://greasyfork.org/en/scripts/38714-steam-store-show-entire-wishlist

Try this:
https://steamcommunity.com/sharedfiles/filedetails/?id=1746978201