deleted file is still listed in 'files' database table

simplified the question

With regard to question #1:

I tried modifying mm_s3 to delete the entry in the 'files' table, when the local file was deleted. Specifically, inside the function mm_s3_send(), I replaced:
unlink($delete_file);
with:

$success = file_delete($delete_file); // Calls unlink(), then returns SUCCESS
if ($success){  //If the file was successfully deleted, update the database
  db_query('DELETE FROM {files} WHERE filepath = "%s"', $delete_file);
}

Unfortunately, I now get this warning message on the node-form:

warning: array_merge() [function.array-merge]: Argument #2 is not an array in /mysite/sites/all/modules/filefield/filefield_widget.inc on line 255.

Presumably, mm_s3 was doing the right thing by not deleting the entry in the 'files' table, even though the local file had been deleted.

Again with regard to question #1

I just thought of another reason not to delete the entry in the files table, when a file is moved to s3. Filefield uses the 'files' table to handle potential file-name collisions. For example, if a user uploads 'test.mp3', but a file with the same name (and path) was previously uploaded, then filefield renames the second file to 'test_0.mp3'. If the files on s3 were not listed in the 'files' table, then filefield wouldn't know when two different files had the same name.

With regard to question #2

I modified the function media_mover_api_node_update($node), in media_mover_api.module, to delete the file-listing from the 'files' table, when the user has deleted a media-mover file.

I replaced:
media_mover_api_file_delete_call($mm_file);

with:

media_mover_api_file_delete_call($mm_file);
// patch:  delete listing from 'files' table
$fid = $mm_file['fid'];
db_query('DELETE FROM {files} WHERE fid = "%d"', $fid);

Note:
I submitted a patch that includes this fix. See http://drupal.org/node/1478246

Regarding #2:
I am storing files in a multi-valued filefield. The user edits the node, deletes the file from the filefield, and then saves the node. The file the user just deleted is still listed in the 'files' table.

Does that answer your question?

The patch here fixes this problem: http://drupal.org/node/1478246#comment-5893866

clarification