What is the best way to mark my new or recently scanned data as viewed in the Content Manager Database?

When you do your initial scan to place your content into the Content Manager Database, all the new items are marked as new (or new to the database), This means that they will all be highlighted or marked as "not viewed". If you have large data sets, it's recommended that you browse to sub folders and select a folder then right mouse over the folder and "mark as viewed" this will clear a smaller set of content. If you try to do the top level directory to "Mark as Viewed" it may take a while to change the display state.

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