Have you inadvertently entered private browsing mode? Is the toolbar on the bottom of the Safari window white on black?
If this is the case, exit private browsing mode by tapping the multi-tab icon on the bottom toolbar, and then tap the word "Private."
Check if you have opened the "Private mode", if you are using the "Private mode", safari won't keep your reading history.
Seems like that was just covered in the last few posts.