NO, what ever you do dont just file them, there is no way on this planet that you can file them right, the centre bore is there to surve a purpose and that purpose is to centre the wheel, so please do not just file it.
You could file the wheel bigger than the hub-flange, the wheel nuts will centre the wheel, but you won't benefit from the support the flange gives to the wheel, although I suspect most alloy wheels will also have a centre bore bigger than the hub-flange anyway.
The wheels are dirt cheap anyway and besides I can probably get my bro-in-law to bore the wheel centres if I do have a problem.
Thanks for the heads up guys...