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.