Background: On iOS, it's possible to keep riding in the same session/instance of Zwift without completely reloading the app, due to how iOS keeps apps running in the background.
If you enter a mission on a course one day, the course changes, and you enter the mission again in the same session, your second attempt will not count.
We're working to fix this in an upcoming update.
In order to avoid your efforts going to waste - and just as a general good practice - we recommend force closing the Zwift app before starting a new session. Instructions for this are on Apple's website.