Why does Automator not see new files in subdirectories on a Flash Drive?
"The Filter Finder Items action uses Spotlight. Having success after using an item with Numbers.app would suggest that the (newer) external files have not been indexed (yet)."

Thanks!!  I modified the Automator app to remove the "Filter Finder Items" action (I put this functionality into the Shell Script)
so now I have:
   “Get Folder Contents” (‘Repeat for each subfolder found’ is checked),
    followed by a Shell Script (which compares the names of the files on the flash drive to the names of the files in the destination directory, and acts on those files that do not exist in the destination directory).

And this works just fine, no files are left out.