When I update a book downloaded from the Apple book shop, the book is replaced in my library and all my notes/highlights/bookmarks are moved to the new version. https://books.apple.com/gb/book/take-control-of-devonthink-3/id1615291486
When I import a newer version of an epub, it’s imported as a separate book. https://www.takecontrolbooks.com/devonthink-3/
Any workarounds?