I haven't done any investigation to determine where the actual bug is here (perhaps it's in the embed question filter). But I have verified that this problem does not occur in Moodle 3.9. To reproduce:

On a 3.9 site:

1. Install the embed question filter and atto plugin:
   • git clone git@github.com:moodleou/moodle-filter_embedquestion.git filter/embedquestion
   • git clone git@github.com:moodleou/moodle-atto_embedquestion.git lib/editor/atto/plugins/embedquestion
2. Browse to "Site administration" > "Plugins" > "Filters" > "Manage filters"
3. Enable the "Embed questions" filter
4. Browse to "Site administration" > "Plugins" > "Text editors" > "Atto HTML editor" > "Atto toolbar settings"
5. Under "Toolbar config" find the "other = html" line and change it to "other = html, embedquestion"
6. Press "Save changes"
7. Create a course
8. Create a question category with an ID in the course
9. Add a question with an ID to the category you just made
10. Create a book
11. In the description, expand the atto tool bar using the button
12. Click the button and select the question and category you made from before
13. Press the "Save and display" button
14. Fill out the form for a book chapter and view the book
15. Everything looks fine
16. Upgrade the site to 4.0
17. View the book
18. The question will be duplicated over and over on the page