First of all, “rail dust” if removed properly does not come back.
Rail dust is exactly that, when cars are transported by train (rail) from the factory to a city, the metal wheels of the train cars running on metal rails create small particles of metal that fly into the air and land on the horizontal surfaces of the car.
They are hot and will adhere to the paint. Then when they get wet from rain; snow or just dew they rust and create tiny little rust spots which are quite visible on white, yellow, beige or light colored cars.
The proper way to remove them is to soak towels in “rail dust remover” and lay the towels on the offended areas of the vehicle. Follow the manufacturer’s recommended dwell time to allow the chemical to dissolve the rust spots and loosen the particles of metal.
When this is accomplished rinse off the car with high pressure water to ensure all particles are gone.
Then pre-spray the car with a mild alkaline cleaner to neutralize the acidic rail dust remover. If you do not do this, acid will remain on the paint finish and when it gets wet it will be active and could etch into the finish.
Then rinse off the alkaline chemical and follow that with a thorough hand carwash using a mild carwash shampoo and water.
To be safe, a coat of wax or paint sealant should be applied to the paint for protection.
Never use clay to remove rail dust because all that does is break off the tip of the metal particle, leaving a part of the metal still on/in the paint and when it rusts the spots will come back. If a paint finish offended with rail dust is properly treated chemically, then that should solve the problem.
You certainly do not want to repaint a vehicle unless you are absolutely certain there is no rail dust residue on the car. Of course, a competent paint shop would insure this to be the case before repainting.
If a detail shop, auto dealer or body shop attempted to remove the rail dust and it comes back, it is a good assumption that they do not know know what they are doing, or implemented the incorrect process.