We still have 1000 year old codex in quite good conditions. A paper book will still be readable 500 and 1000 years into the future, if properly stored. A digital file will be effectively lost in decades, if not mere years.
Millennia old codices are extremely rare, and they've survived either by dumb luck or because they were treasured.
Maybe OP is a famed thinker, whose disciples will carefully preserve their notes; or their house is in a cave that will be at sealed in a landslide; or they will die in a peat bog clutching their notes to their pallid breast as the life force seeps from their body, submerging them in preserving ooze...
When I draw something I can remember the shapes better than if I simply sit there and stare at it. Something with the hand-eye coordination triggers the brain into remembering.
Typing in contrast, one is not tracing the shapes of the letters (the thing to remember), but pushing buttons that are not physically related.
It’s the same thing as if you can touch and hold an object it becomes much more real than if you can see it in a picture or on a screen. Remembering is connected better to touch.
The primary activity of note-taking is forming words and grappling with ideas, though — it's not like all benefits are lost when using a keyboard. To a certain extent other activities like typesetting achieve similar ends.
My brother writes novels longhand, and I've thought hard about this topic. Ultimately, certain personality quirks held me back and I never felt carefree when hand-writing notes. Version control liberated me.
I've also started collecting fountain pens, so it's linked to a related hobby. It's difficult to express that it is the entire experience, from the ink, to the feel of the pen, to what words are being written onto paper, that feels the most rewarding. I've also rather deliberately avoided document inks after much contemplation. I figure that the majority of inks I have aren't waterproof; if the journals ever get wet, everything in them will be destroyed.
That's how I've grappled with the ephemeral nature of the physical. Rather than aiming for optimizing permanence, as best as can be done on tangible, material books, I've preferred to embrace its weaknesses with full acceptance of what can (and will) go wrong. I suspect this is also because I have very little intent to ever go back and read what I've written. That could change, of course.
Enjoy notes the way you want!
But when I re-read a book I’ve previously annotated, I get a rush of the time and place it happened, 20 years later. It’s crazy.
We are tactile beings who exist and connect in 3D space and brains remember ideas in locations.
I love files. But I think strong entities are trying to rip control away, with stupid consequences like making .txt obsolete.
Books have a good chance outlast a)mediums and b)formats. They have a good track record. Check back in 5000 years.