If you are only concerned with eliminating duplicate files, you can use an outside Organizer program to perform the task by deleting them from your hard drive. Once you have done that, you can use the Find>All Missing Files command in the Organizer. The grid will display all files that have been deleted from the hard drive. You can select all the visible missing files (Ctrl+A) and delete them from the catalog.
For safety's sake, you should perhaps also Find>All Missing Files before using the third party program to delete the duplicates. That will ensure that when you use that command after deleting the duplicates, you will only be removing the newly deleted files. Alternatively, don't use the option to delete files from the hard drive when using the Organizer's delete from catalog command.
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