It's the interface and interaction of physical books which is lost.
I can keep my hand between two sections and flip between them, insert colored post-its, or bokmarks or index cards. Dog-ear pages, make marginal notes, star, underline, or (shudder)highlight.
The one thing missing is full-text search, though a good index is a 90% solution (and so: not optional).
Text and other element placement is static, so spatial memory works. Fluid layout is great for screens, but lousy for recall.
And the interface is consistent across books, authors, publishers, and centuries. Whilst, yes, various ebook formats offer facsimiles of many of these features, they are just that, and mediated to bot. Want to highlight? Better hope that's a rendered or OCRd (and reliably) PDF, or you're SooL.
Source; A tablet with over 5,000 epub-type docs, of various sources and provenance, from single page to multi-volume book length. I appreciate the weight and space savings, but miss much physical books deliver.
I remember roughly how far into a book, or chapter, passages are. Where on a page, or with relstion to other elements, how or where a line breaks (especially if that's awkward). Where the book itself lives within my collection. Where I was when first reading (or later re-reading) it. Etc., etc.
Spatial associations.
Consistent pagination is useful, but it's a small subset of the whole.
I generally print out research articles because I can write all over the figures and take it with me to lunch and not be bothered when I spill on it, or fold it up into my back pocket. I feel like I get better comprehension too. For textbooks that's a no go for me and probably most students, because this thing is getting resold once I'm through.
https://bubblin.io/cover/ladakh-by-satie-sharma#frontmatter
Disclosure: I'm the developer behind the project.