To double check I attempted to replicate again by following the steps:
- In M2.5 create a CT course with ten sections.
- Add a 'Book' to section 1.
- Add a 'Book' to section 2.
- Go to the front page.
- Change Moodle core code to M2.6 and remove the 'topcoll' folder.
- Perform the upgrade to M2.6.
- Go back to the course and observe that it has been changed to the default weekly format. Ten sections are shown with no orphaned activities.
- Install CT.
- Go back to the course and edit the settings to set CT as the course format.
- Observe that section 1 and 2 both have the same Book resources added originally.
Therefore cannot replicate the issue.
The only course format I know that could possibly have this issue is the Flexible sections format (https://moodle.org/plugins/view.php?plugin=format_flexsections) where when changing to another course format the contents of the nested sections can become orphaned.