Do you have duplicate images?  Here is how Tag That Photo handles them (today).  We create a signature on each image (the pixels of the image and not the metadata) so we can tell whether an image is a duplicate.  If we find duplicates, we only edit metadata and face tags on the "set" of duplicates.  So if you add a face tag "Mary" to one of the images - it will be written to ALL of the images.

There are some situations where a person's organization structure forces duplicates.  For example, let's say that Mary and John are in the same photo "image001.jpg".  Some people like to keep a copy of the image under a folder named "Mary" and another copy under a folder named "John".  In this case duplicates are wanted!

However, there are other situations where you want to remove duplicates - and there are a variety of programs that can be used to remove duplicates.  The advantage that some of these programs offer is finding "similar" images - including ones that have been downsized or with slight modifications to color or brightness for example.

This list is not exhaustive, and a few Google searches may find some others:

If you delete duplicates, as long as at least one of the images remains under a monitored Tag That Photo folder, then your metadata is safe.