There is a Sitecore administration page that allows you to remove broken links. You can find it here:
http://localhost/sitecore/admin/RemoveBrokenLinks.aspx
You simply select the database and complete the action. You can also serialize all items modified during this process.
You may need to change the timeout settings in web.config :
<setting name="DefaultSQLTimeout" value="10:00:00" /> <setting name="DataProviderTimeout" value="00:00:00" />
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