If it is just surface rust then removal of the rust and rust prevention treatment should suffice.
For steel to rust the primary ingredients are moisture H2O and Oxygen O2 which combines to form FE2O3 Rust. Anti rust treatments if applied correctly inhibit both moisture and oxygen reaching the steel thus preventing the rust from forming.
The problem then is any gaps or cracks in the treatment allows the rusting to recommence except now it creeps under the treatment unseen so requires regular monitoring and remedial action.
The biggest issue is structural rust in sills is when it eats through the metal from the inside out due to the box section design, this is no longer surface rust as a poke with a screwdriver or an official MOT hammer will soon reveal