For years I took notes both with pen/paper and digitally, and either cross-referenced things or scanned pages into a master digital document like you describe. For me, the game-changer has been getting a RocketBook. It’s handwriting recognition is about 98% accurate for me, so it only takes a few minutes for me to scan some pages, drag the emailed text file into VS Code, join lines into paragraphs, and check for typos. Gives me a chance to review what I wrote too. Then it goes from there into a plain text file (or more recently, WorkFlowy) which is my preferred system. I started with the free PDFs that RocketBook makes available, but finally bought one mostly because I wanted to pay for their server resources. :-)
The RocketBook is actually what got me started on this. My pen died, so I started using the OneNote app (service provided by my employer) and it's worked well enough. I definitely recommend the RocketBook.
