[davidfor]

That sounds like an error in the code in the book. The calibre viewer is not good for finding this sort of thing as it tends to handle the error quietly and display the book. If this is the case, the error checking in the calibre editor might show the error. Or Sigil might if you prefer that. An epub-to-epub conversion will probably fix it.

There is a case that I haven't quite worked out that annotations can cause a problem like this. What I think is if the locations in the annotation no longer exist in the chapter, they will cause this problem when you try to go to that page. I don't think this will have an effect on navigating to a later chapter, so that might not be the problem here. But, if it is, deleting the annotations should fix the problem. And using the Annotations plugin shouldn't cause a problem. It only read the annotations from the database and doesn't change anything on the device.

If you want to send me the book, I'll have a look and see if I can see what is wrong.

Edit: OK, it was fixed by going back to the original source. Maybe something corrupted it the last time and that has been fixed.

The annotations reappearing is expected. For epubs in the main memory, the annotations are written to an annotations file as well as the database. Deleting the book does not remove this file. And the file is linked to the book by the file names of both. When you opened the new copy of the book, as the file name was the same, the annotations file was read from the annotations file.