Deleting pages

Physical pages in InDesign are one layer. Document pages are in a text flow that lies on top of these pages in text frames. Deleting a physical page won't change the flow and order of the text frames and content; deleting a text frame will just leave an empty physical page and push all the content down to successive pages.

In general, don't mess with the physical pages defined in the Pages pane. And don't delete the frame on any document page. If you have an extra page, you have to delete all of the text-flow content in the frame on that page to get all the following pages to move up. Many times there are hidden characters, page-break paragraph styles or the like pushing text down even though a page seems to be empty.

But work entirely within the text flow to "delete pages." That's very simplified, and there are times to delete frames and physical pages, but I think you'll find this accomplishes what you're after and makes the "content logic" a little clearer.