@gwarser Unfortunately there's no way to delete watch-later data from user scripts as far as I know, only save it. A "work around" is to re-open the movie (mpv removes the watch-later data when you open the file), then ctrl+c out of mpv, which should exit without re-creating the watch later data.
It might be worth opening an issue to request a way to remove the watch-later data programmatically.
You can (ab)use the undocumented mp.find_config_file() to get paths to files near or about the mpv executable or config directories. Here's how mp.options uses it - if you replicate the MD5sum process for generating the watch-later filename, you can find_config_file it and remove it (or, if lazy, clear all files in the watch_later directory).