It's fine, the screws don't hold the rotor on the hub, it's the lugnuts that do that. The screws are only helpful in keeping the rotor stationary so it's easier to put the caliper back on. Some aftermarket rotors don't have holes or have malaligned holes. In fact lots of guys I know didn't replace the screws even when the holes do line up just because they can be a PIA to get out.