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I've been using spot putty on all the little chips that the heavy-rust primer didn't fill and there are TONS of them. Anyone have any tips for this kind of thing?



The preferred method to get rid of chips is to sand them out and feather the paint as necessary. Primer does just like you found, shrink. Spot putty will too. Even if it looks good when you get around to applying paint, it will still shrink a little more over time. One of the things that makes for good prep work is little details like that.