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I don't use the automatic archiving function, preferring to archive by hand. However, a quick experiment on the default database suggests that a dropped folder with otherwise active projects in it doesn't get archived. It may even be that dropped folders don't get archived at all; I didn't test the more general case. If I'm wrong and it gets archived, you can simply open the archive and drag the folder back to your main database. I don't know how often you archive, but you could also just mark the folder as active before archiving.