I couldn't use it, that was the point - Joomla uses a Session object and the database, but I needed simple sessions without Joomla.
Anyhow, I have finally worked it out. The code below will end any current session and set the session handler back to default. It will then open the session. Strangely, I'm sure I tried this before without success, but it now works perfectly.
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@session_destroy();
ini_set('session.save_handler', 'files');
session_start();
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