What you’re seeing is really an artifact of the old Observable design which did not allow you to replace files; you could only add new files with new names (hence the @2, @3, @4, etc.).
In new Observable, when you replace a file, it actually gets replaced (for subsequent versions of the notebook)! You can also delete files without breaking old versions of the notebook. And you can rename files to whatever you like (again, without breaking old versions, and it automatically updates your code to match).
Old Observable tracked which files you referenced to show “unused” files because of the limitation that you couldn’t rename or replace files, or delete them without breaking old versions. We could show you which files are unused in new Observable, too, to help with the transition, but ultimately we don’t believe it’s necessary because there’s no reason to accumulate unused files in Observable (as you can actually replace and delete files).
You can also access the old interface at old.observablehq.com, if it helps.