rust

I've been recently told by a garage mechanic/engineer that you have to be carefull when removing rust as it sends out runners under the paintwork that you can't see. Its important that any rust patches are taken back to bare metal before treating which includes taking back the surounding painted areas. You can get rust treatment that changes it to a chemically inert state.
Personally I find it better to remove all rust and fill any small holes either with filler or with weld before treating and respraying. Its a pain of a job but I think will last longer in the long run.