After completing the project, without creating a new project. You start adding new files to an old project, and you continue to work on something. At this time, duplicates begin to appear. Make it a rule to start any new job by creating a new project.
It is unclear after what time and why duplicates begin to appear. Just don't do that, and you'll forget about duplicates.
Above, I described how to change something in old projects. Open the old project and save it. Without leaving the program (important). Create a new project. Save the old project and work with it. After creating a new project, the old slide loses its dependence on the old files and archives.
If you have duplicates, (CtrlZ) will not help you to delete them. Because. (CTRL+z) Cancels the action, but the connection to archives and old files remains.