Proofreading is almost always the last stage before you publish your book, and proofreaders often should find very little. They were traditionally there to focus you on layout, punctuation and the odd misspelled word. And they are important as an impartial set of eyes that will ordinarily spend less time with your book than your Story and/or Line/copy editor.
Proofreaders can also look at cleaning up format before you send it to your formatter, or upload it yourself to D2D or another site that converts documents. Be aware that skipping a formatter is possible, but if your file is a mess, a very bad idea. You should clear ALL corrections, all notes, and ensure that every page has correct margins, the same font and consistent headers.