If you have a course with course completion enabled, and users have completed one or more of the criteria you have to click Unlock completion options and delete user completion data. You can then edit activity completion etc. and click Save changes.
However, if the site cron runs after clicking Unlock completion options and delete user completion data but before clicking Save changes then the changes you make are not saved. There's no error, it appears to work when you click Save changes however, if you then return to Course administration -> Course completion the changes are as before.
Issue present in 3.1 (originally seen in 2.8.12).