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The best way for future links is to create universal redirection links (domain.com/code/). That way you only need to change one place (for instance in database or .htaccess). If you have control panel on your server, you can probably also do it there. Or you can create universal php includes for the links (just like creating standard templates).
If you want to change existing links you can download the db's and do a bulk replace. I use UltraEdit to do bulk editing.
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