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I tried redefining the \FancyVerbLine to have a \large, but that didn't help. Is there another way to do this?

+1  A: 

That should do the trick. How exactly does your \FancyVerbLine look like? Notice that it’s not enough to put the formatting in – you also need to include the counter command:

\renewcommand\theFancyVerbLine{\large\arabic{FancyVerbLine}}

This should work.

Konrad Rudolph