My Confluence instance has 50,000+ rows of hardcoded links. Is it possible to change them with an update script (SQL Server 2008) using __ATLASSIAN_BASE_URL__? For example
SET DESTPAGETITLE =REPLACE(DESTPAGETITLE,'//hstnwikiweb','__ATLASSIAN_BASE_URL__'
BODYCONTENTSET BODY =CAST(REPLACE(CAST(BODY ASvarchar(MAX)),'//hstnwikiweb','__ATLASSIAN_BASE_URL__')AStext)
I'm not sure whether the SQL would work for you or not, but you could certainly take a backup and give it a try. However, when I read the title of your question my first thought was that you should export your data to XML, open it in a text editor and use the Find+Replace function to replace the URLs and then re-import the data. So, in the event that the SQL doesn't work then try editing the XML and see whether that works for you.
All the best,
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