IF you have FileMaker Advanced, you can give the data entry layouts a custom menu where duplicate record has been removed or just modified so that it no longer has a keyboard shortcut. I've removed the keyboard shortcut for deleting records from a few layouts for similar reasons. (So supervisory personnel can't accidentally delete a record via shortcut.)
You can also provide a "delete" option that doesn't physically delete a record but instead sets a value in a field so that scripts, finds etc no longer pull it up on the usual data entry layouts, but it's still in the system. That allows an admin person to find and "undelete" the record on occaissions where this is needed. If getting a large number of "deleted" records in your table is a concern, you can set up a script that deletes them after they are specified number of days old such as 60 days after being marked "deleted".
Thanks, Phil. That's exactly what I needed to know.