Youtube seems to not always mark videos that I've watched a while ago. This can be quite annoying. To fix this, I tried using the Watchmarker browser extension. However, it does not seem to be able to pull in all watched videos from the Youtube API either.
However, when you download your data from Youtube (using Takeout) you get a file watch-history.html, which does contain your proper history.
To load this into Watchmarker, I wrote this program, which takes in watch-history.html and converts it into a watchmarker-youtube.database file, which you can import into Watchmarker using the Import button.
To run this program, first install Rust, then check out this repository, put your watch-history.html in the repository directory, run cargo run --release, and finally import the resulting watchmarker-youtube.database file into Watchmarker using the Import button on its Settings page.
Note: when importing you might have to explicitly select Options > Format > All Files in the Import screen on Mac OS X.
Limitations: this program currently does not support importing the actual date or number of views. It always shows up in Watchmarker with a hardcoded date, and with exactly 1 view.