I wonder if the effect diminishes if the digital media is more like paper, as with e-readers, or if it is due to other differences like scrolling versus page turning.
After years of taking notes in paper and e-ink and keyboard, I love paper because of the spaced repetition that's forced when I'm scanning back for old entries in a notebook. It is probably the root of all my memorization and free association.
Whether I'm "bookmarking" e books or trying to do clumsy search for old entries, I think I pick up a lot just by seeing the notes again by accident, feeling the page, or something else. Can't say but it's nowhere close for me with electric media.
The main claim is that digital media remove the spatial element from the picture, making it more difficult to remember things. This isn't a crazy notion. Think of the method of loci[0] which explicitly uses an imaginary space to "keep" information for later recall. This must be, because spatial association is something useful for navigating spatial environments, so if you cannot lean on that to reinforce memory and recall, then you're at a greater disadvantage.