I've been distraught at the same thing. I had a few playlists that I grew over time, and it's annoying to go back and see gaps of "[Deleted video]" where your favorites used to be. I'm curious to know if you've found a solution for this.
Personally I've started locally saving anything I think I would want to watch or reference again. When favoriting something or saving it to a playlist, I download it too. I started off with using youtube-dl on the command line and have experimented with the "Import from YouTube" function on Peertube but ended up with a tiny cobbled-together video platform, importer (youtube-dl wrapper), and Firefox extension. I think the next step will be easily saving non-video things - probably recording WARCs?