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Our carrier high efficiency gas furnace was not checked for many years and has internal rust on panels due likely to a clogged drain tube causing condensate to drip inside furnace (see photos). No AC in system, this is heating only.

We will figure out the leak cause and fix it, but what should we do about the rusted metal panels? Ignore the rust? Somehow remove some or all of the rust? Chemically treat it?

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If you resolve the root cause, namely moisture, then it should be stable. You could apply some "rust reformer" and then paint the surface but only if this rust bothers you.

If you are still having moisture buildup inside the cabinet, then you should resolve that.

Rust, on its own, forms a protective coating that keeps the underlying steel from continuing to rust. But in the presence of moisture additional rust forms and flakes off the coating and you eventually have the metal compromised.

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