That command removed the old database file that’s why the first step in the guide is to make a copy of the database.
For your issues.
1 - It’s likely the added at date for that movie is sometime in the future. Recently added sorts by the newest date so these will always be in the front. Plex Dance the file and this should get fixed.
2 - This might be normal. Without more details it’s hard to say. One thing you can try, if you haven’t already, is to optimize the database.
3 - I have no idea what that is for so I can’t comment. Please note that the Plex database does change from time to time. If that script isn’t maintained, it’s possible it can stop reading the database file even without any data corruption.
