So I finally was able to replace my rotors after I drilled out the rusted screws that hold the rotor in to the hub. To avoid this problem in the future I did not install those screws/bolts back in. Is this something I should not be doing or is it okay for me to leave them like that? The vehicle is a 2005 Honda Civic HX model.
Those screws only hold the rotor in place to match the holes for the bolts holding the wheels, and/or to stop the rotor tilting when changing a wheel. Just makes it easier when having to hold a wheel with one hand and fit wheel bolts with the other.
The diameter of those screws is not designed to hold the rotor under full braking force as they will shear.
So, I would get new ones and fit them, some rotors are sold with new screws anyway.
The function of the screws is to locate the rotor in the correct position while building up the complete wheel assembly. The rotor is actually clamped in place between the wheel and the hub, but the wheel bolts don't position it accurately.
If you leave the screws out, you might end up with the rotor off-center and unbalancing the wheel, causing vibration.
A better design (making it impossible to assemble incorrectly without needing the screws) would be to have locating pins that were an integral part of the rotor, but that would be too expensive for auto engineering!
Since the screws don't carry any load once the wheel is in place, you can use as much grease, WD40, etc, as you like when replacing them without worrying if they will work loose, and they only need to be tightened enough to locate the rotor in the correct position.