Could there be a Preference Toggle to disable duplicate checks? Like many people who manage very large databases of stored documents, I often have documents with the same filename but very different content. I am meticulous about filing structure and my workflow would never result in an actual true duplicate, though many similar documents might have the same filenames, but have been stored in a multi-depth filing structure. When importing these items into DEVONthink, if it thinks, based on the filename, they are duplicates, it doesn’t import any but the first, seeming to make a reference to the first imported in any other locations in the database. I would rather DEVONthink not even consider whether items are duplicates.
Did you try turning on stricter duplicate detection in the preferences?
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The filename actually doesn’t matter, only the contents of the documents. And importing doesn’t skip files.