I rarely have that problem with watch later, but it does happen. When I want to ensure a video is available down the line, i send the url to the web archive; they have a special archiver for youtube videos.
Example: https://web.archive.org/save/https://www.youtube.com/watch?v...
If it's already saved, it'll do a new snapshot, but I believe the archive is smart enough not to duplicate saved youtube videos.