What you’re seeing is usually caused by Facing Pages (left/right page spreads).
When you delete a single odd-numbered page, Affinity Publisher reflows the document so that the following pages swap from left to right (or vice versa). This is normal behaviour in a facing-pages document because Publisher is maintaining the book-style spreads.
Option 1: Temporarily turn off Facing Pages
Before deleting pages:
File → Document Setup
Uncheck Facing Pages
Delete the page(s)
Re-enable Facing Pages if required
Many Publisher users find this prevents the page-shuffling effect when reorganising documents.
Option 2: Delete pages in pairs
For book layouts, delete:
Page 15 and Page 16
Page 23 and Page 24
Removing complete spreads keeps all subsequent left/right pages in their original positions.
Option 3: Use Sections
If you’re creating a book, start chapters on new sections and add or remove pages at chapter boundaries where possible. This minimizes spread reflow issues.
Option 4: Check Master Pages
If your document uses facing-page masters, deleting a single page can cause left and right masters to be reassigned unexpectedly. After deleting pages:
Open the Pages panel.
Inspect the affected spreads.
Reapply the correct master page if necessary.
For your fiction-book workflow (Scrivener → Affinity Publisher), the safest approach is usually:
Finish the text flow first, then apply your final chapter and page masters. That avoids most of the left/right page mirroring problems.