Yes. You can manually add/update/delete a document/URL through the admin console for an HTTP or File System collection.
To add a URL to your HTTP collection, enter the web address and click "Add/Update":
To delete a URL from your collection, enter the web address and click "Delete":
To see the status of a URL, click "Status":
To add a file to your File collection, enter the file name and click "Add/Update":
To learn about manually adding document in a HTTP collection read: Add Document for HTTP Collection