If you have user scenes that you don't want to lose I would recommend coming into this screen and clicking the button to "Fill Missing Timing". This will ask you which player to use and it will briefly start each user scene that doesn't have a start time recorded yet in its metadata. That way, in the future, if that user scene gets removed (most likely during a movie update) then you can come back into the Scene Shot List and you'll see that the scene is now missing. But since we have the start time and duration, we can attempt to reshoot the scene. If you start a scene reshoot and the total runtime of the movie matches the old total runtime of the movie that we observed, then it will recommend an auto reshoot. Popcorn Ready will ask which player to use and it will automate the process of playing the movie and finding the start time and then starting the new scene, playing for the correct duration, and then ending the scene. Then it will rename the scene back to what we had archived in our Scene Shot List.
Then, if you had used that user scene in any scripts, go into the Script Writer and find the script and you should see that step was unavailable. But you can now click Rewrite and it should repair your script and update it to use the new scene that you just reshot in the step above.