Is this in 5.6?

5.6 introduces a new feature which automatically adds a portal alias if you 'hit' the site from a domain which isn't already in the list of portal aliases.  This is designed to stop many issues that arise from returning 404 errors when a domain/alias mismatch has been introduced by changing domains/migration of sites from dev to live, etc.

It's possible that this is how you caused the issue in the first place.

In terms of fixing the aliases, you can always edit the records in the database directly (in the portalAlias table).  The first alias is always locked so you can't remove all the alias entries.  But there's nothing to stop you removing one of them directly in the database, as long as you're careful.  You'll also have to restart the site by touching the web.config to make sure all the cache items are cleared - you don't want the site to still think the 'missing' alias is still valid.

You need to reload your web.config file to make the change..

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