Quoted from Pac-Fan:
Absolutely. Anytime you have rust, no matter how you take it off, any protective coating that was there is gone. Evaporust (used correctly for the correct amount of time) doesn't eat off *additional* protective coating like other more harsh chemicals but the damage was already done with the rust. It will re-flash rust in time, from hours to days to weeks to a month, but it does.
I have run many things through it from chrome legs, drop target and flipper assemblies, above PF stainless steel, lock down bars and the like. It will look better and won't egregiously rust looking like it did before cleaning, but make no mistake it will re-rust with a thin coating in most cases. You will need to seal with oil, grease, paint/clear-coat or re-electrolicize with a inhibitor of some type if you want it to keep the just-cleaned look.
I've got things I've run through Evaporust nearly three years ago, and they look exactly like they did the day I took them out of the bath.