[davidfor]

Originally Posted by MacEachaidh

That's what I was expecting, but as I said, that isn't what is happening. Even when I manually delete each annotation before removing the epub file, they're back when I sideload the new version of the book. I tried deleting the annotations manually, then adding new highlights in different spots, and after the book is replaced I get both sets of annotations being reinstalled.

I do roughly what you are saying all the time and the annotations disappear. Usually, I'm only fixing spelling and styles, so simply replace the book. But, I recently had to fix the ToC and split some files, so I deleted it that time. The annotations didn't reappear after this.

Unfortunately, this sort of behaviour usually means the database is corrupt. But, as a last check, try restarting the device after deleting the book and before connecting. That will reread the database and might fix things or show more problems that will mean you need to create a new database.

At this point, the book isn't substantially changing, so I haven't come across the problem of the annotations being put back in the wrong place.

If you are just fixing spelling or styles, you shouldn't hit the problem. But, if you change the structure, or remove a section that a annotation is in, you might see the hang. From memory, the last time I saw it, I had highlighted the last couple of paragraphs in a section and then merged them together. In that case, the location for the end of the annotation didn't exist and that caused the problem.