When you upload a file or view an existing file in your media library and see, the URL / path of the file is not synchronized with the folder but it states “File is synchronized physically”, this can have different reasons.
The WordPress core must know the current owner of the file at the time of calculating the physical path. For example, if you upload a file via the WP CLI command
wp media import, this file has no owner.
There are two solutions:
- Update the author of the media file by WordPress core API through custom coding
- Use a plugin like Bulk Change Media Author (outdated, but still works)
Cause 2: Symlinks
Unfortunately, it is not possible to handle symbolic links with Real Physical Media.