Is there no way of modifying the board such that you feed that bank with the right voltage?
LVDS output signals will simply be a little misshaped. Being a current based signalling standard, the IO circuitry - driven at 3.3V - will be able to drive the rising/falling edges faster. They're unlikely to damage the Cyclone IV and it will most likely just work. However, you will be operating your devices out of spec. So, Altera won't support you should you suddenly start burning out parts - something I think unlikely to happen but it's still a potential issue.
Cheers,
Alex