We are encountering a similar problem when restoring older courses with user data.
When the users have been deleted (but are still in the user database according to our technical support), they do not restore when courses are restored with user data. The user data is in the course backup files (versions 2.3, 2.5, 2.6).
When I research the Moodle docs, I found these links which suggest that user data can be created on restore:
https://docs.moodle.org/27/en/Course_restore
https://docs.moodle.org/27/en/Capabilities/moodle/restore:createuser
https://docs.moodle.org/27/en/Capabilities/moodle/restore:configure
https://docs.moodle.org/27/en/Capabilities/moodle/restore:userinfo
But our technical support also found:
https://docs.moodle.org/27/en/Browse_list_of_users
Warning: Deleting an account results in user data being permanently deleted. If you wish to retain any data, you should instead suspend the user's account.
If an account is deleted by mistake, it can be partially restored by resetting the deleted flag to zero in the database and resetting the username and email address. User profile details, user preferences, enrolments, and group and cohort membership data cannot be recovered. Grades may be recovered by re-enrolling the user into their courses and ticking the 'Recover user's old grades if possible' checkbox in the enrolment options. Forum posts are not deleted.
We are on 2.7