Lynn, this looks to be a bug. The Files webpart should not list files that were deleted via the File Manager (ie when you click the "Manage Files" link).
I have opened an issue in our bug tracking database about this problem (see
https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=11396 if you would like track the progress).
The only work-around for this problem is not ideal. You can add the Files webpart to the center pane (ie the wider section of the page). This webpart will display the files using the File manager (ie what you see when you click on the "Manage Files" link.
-Brian