Yah, imagine those greedy money grubbing manufacturers wanting you to replace equipment that has been flooded. 1. The electronics on the circuit board have probably been damaged. 2. I only work on gas equipment so this may not apply, the gas control valve has some springs and solinoids, imagine how well those will work after being water soaked. 3. Some of the limit and rollout switches are thermal snap switches, suppose they corroded or got some sand in them and don't trip. 4. The inducer and blower probably have dirt and grit in them, and the bearings may have been damaged.
Every furnace and gas vavle manufacturer has a warning that if the equipment has been flooded, it should be replaced, there is a good reason.
Yet, if there were a problem, you would probably have no problem hiring a lawyer to sue for a defective product.