Relax! It takes a very tiny amount of rust to bubble paint or lift bondo. I've seen a dime-sized spot of surface rust ruin a whole fender's worth of body filler. Eventually you will need to take it to bare metal and get rid of that bondo. If you like making a mess, get your mask and goggles and take it off with an angle grinder w/ wire cup brush. Keep moving so you don't scorch the steel; the paint, bondo, and rust will all be gone in a cloud of fine dust. Hit the area with phosphoric acid to kill/covert the rust (Rust-Mort or Naval Jelly) then clean and prep the metal as if for paint. I prefer fiberglass body filler over bondo (doesn't collect moisture); heating and beating the steel is better for dents; new patch panels are best if there's holes in the steel.
