MacOS – Macintosh HD can’t be opened because the original file can’t be found

Turns out it was just a permissions problem. Since macOS Sierra doesn't give you the ability to fix permissions, I'll just post this here in case anyone else needs it:

To reset permissions from the terminal:

diskutil resetUserPermissions / $(id -u)

As a (temporary) workaround, I'd use the find command.

In a new Automator workflow, add the following actions:

• Run Shell Script

  • Settings - Shell: /bin/bash and Pass input: to stdin

  • Replace the default cat with:

    find "$HOME/Downloads" -maxdepth 1 -type f -mtime +30d -iname '*.*'
    

• Move Finder Items to Trash

• Save the workflow as an application.

Note: As coded, this only deletes files at the directory level of ~/Downloads. It does not traverse subdirectories, so as to avoid deleting something Safari is downloading at the time it's run, as it uses a .download bundle which is a directory. You could devise a more complex find command and or workflow, however this, as is, is better then your current nonfunctioning workflow.