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When an item has MODS created using the MODS editor, those MODS elements replace the MODS elements created for that element by running a crosswalk (and if the crosswalk uses the File/Folder Name Matcher).
The MODS editor-created elements override the crosswalk-created elements in both the properties pane and the METS export.
If the editor-created MODS elements are removed by using the "Delete MODS Descriptions" menu item, the crosswalk-created elements reappear in the properties pane.
It seems like the properties pane and the export should merge the elements from both sources?