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1) Go to admin—System->configuration->web->Unsecure and Secure
2) Make sure your categories as listed under Catalog->Manage Categories are in the same Root Category as listed under System->Manage Stores->Store Name->Root Category
Holy crap, I was just messing around changing the root folders of stores / categories, now the whole site is botched. Every page comes up as a 404 error, geez. Anyone ever have this happen? Kind of scares me if I can render my site irreparable through a few changes on the admin panel.