I recently found this Watchtower extension and it seems very useful, however I am having issues that when I remove files in Windows, Premiere gets confused and it becomes more hassle to find and remove the files in the project than to not use Watchtower at all. Folders are not static like a statue, things get added but also deleted, renamed, and moved around.
Currently there is a force sync button, maybe there could be another button to force a two-way sync so that files that have been removed in Windows are also removed from the Project so that Premiere is not looking for them anymore. This way it would not happen by accident but only as a result of user intervention to remove the orphaned files from within Premiere.