I keep notes in Obsidian...but when I'm genuinely studying a text I write out a precis as an outline in my bullet journal, and later transcribe it. That means that I engage with the material at least twice: once when I first read it, and once when I transcribe it. And yes, writing it by hand genuinely does help. And then, when I want to look at it later, my original notes are in my journal, and my transcription is available digitally.