First of all, make sure you check your IIS settings to be sure you're calling the right URL and virtual directory that you originally created.
Then, to be sure, run this query against the database to make sure that you indeed have deleted the PortalAlias.
SELECT * FROM [dbo].[PortalAlias]
If your portal alias is not there, add it with this query:
INSERT INTO [dbo].[PortalAlias] (PortalID, HTTPAlias) VALUES (0, 'localhost/dotnetnuke')
My previous example assumes that your local site is "localhost", and your virtual directory in IIS is named "dotnetnuke". You will need to verify the site name, port number, and virtual directory in your IIS instance.