To expand on what I wrote above:
1)
Despite the problem fixing itself for EPUB files, it should save it correctly from the beginning.
2)
I've actually analysed this at database level with the EPUB, before and after quitting the book, and I could see that the value of
ContentID in the
Bookmark table had been updated.
After making the highlight and before quitting the book, the value ended in
Code:
file:///(...).xhtml#idParaDest-40
.
After quitting, it has changed to
Code:
file:///(...).xhtml#idParaDest-41
.