I think my problem is that I've fallen in love with the craft of making books. Working seven day weeks endlessly turning my manuscripts into bound paper copies that are as good or better than my competition on the bookshelves, I've learned so much this past couple of years. I've learned publisher lore, and that's a different thing than what a reader consciously sees.
Let's take one example; scene breaks. Everyone knows what words, sentences, paragraphs, and chapters are. But if you mention a scene break, the person across the table nods, but has a puzzled look in their eyes. I guess it's because it isn't really taught in school. Let me explain, at the risk of causing other writer's eyes to glaze over.
A scene can be thought of as a sub-chapter. Something changes in the narrative; time passes, the viewpoint character has shifted; the pacing of the action has abruptly shifted. Now, if a reader is scanning down the page, paragraph by paragraph, and there is no visual cue that the scene has shifted, then an action description of Jane's actions may be confused with Dick's, leading to the reader stumbling over the words and being knocked out of the story. But sometimes, you don't really want a big sub-chapter heading that might in itself distract the reader. The publisher needs a more subtile way to cue the reader that something has changed.
Now, for decades, I've been writing manuscript format, leaving such details to the publishing side of the house. I write my paragraphs and then when I need a scene break I leave '###' centered on a line by itself between one scene and the next. Writers and editors know what that means and it serves the purpose.
Ink on paper has hundreds of years practice dealing with this problem and one very common solution is the dropped cap. The very first letter of the new scene is enlarged and shifted down so that the paragraph is still block-shaped. There is often additional white space between the scenes as well. The cute thing is that this method is so common that it's invisible to readers on the conscious level, but they know something has changed, which is exactly its purpose.
Now comes the problem of converting this manuscript into ebook formats that are light on formatting options. In fact, having the reader in control of font sizes and general formatting is one of the benefits of the electronic book media. Tools that used to be the domain of the publisher to be used to make a smooth and elegant reading experience, are now tools the reader needs to make tiny screens readable in poor lighting situations. And what's worse, the formatting possibilities are different from one ebook format to the next. From the publisher's perspective, you can't make a good looking ebook. It's not possible. Most readers aren't even aware that there's a problem.
So back to the scene break. How to give that subtile cue to the reader? Most of the automatic book converter tools I've tried end up stripping scene breaks. Unless you care about confusing the reader, you'll have to wade through the converted text and page by page, fix up the scene break; possibly by putting back a variation of that '###' that the manuscript had in the beginning and hope the reader doesn't stumble over it.
In fact, conversion straight from manuscript to ebook is easier than reusing the paper formatted version. The typewriter has many of the same limitations as the ebook; no font changes for example. I've spent time developing InDesign conversion tools that, in fact, can convert my carefully crafted print books back into a version that will convert more easily to ebook formats, but this is just a stop-gap measure. Kindle and it's like aren't there yet, but some day, maybe soon, ebook readers will find a way to allow publishers to use the hundreds of years of refined craft on the same pocket platform that will allow users to change text size and look to their heart's content.
And then, I'll have to convert my books to work in that market as well.