If the file has been deleted from the hard drive, we would want to remove it's reference from the catalog database.
To remove all files that are currently disconnected, go to File > Reconnect > All Missing Files. When you get the window that shows the search in progress, click the Browse button. In the Reconnect Missing Files dialog, click the Select All button on the left under Files Missing from Catalog. Once all the files have been selected click the Delete from Catalog button right above the Select All button.
