Damage is not always immediately evident when it comes to HVAC systems. They are simply too expensive, though, to replace without knowing that it is damaged.
Look at outdoor components first. Condensing units are fairly hardy, and can withstand some flooding, but if waters climb too high on the unit, there is the potential for real damage. If you aren’t sure exactly how high the waters got, in relation to the condensing unit, look for dirt or debris in the fins. Most likely, this will provide a clear line, above which there is no debris evident, suggesting that the water didn’t climb above that point. If the water reached more than two or three inches above the base of the unit, then it should be carefully inspected to ensure no lasting damage was done. If the water rose higher than the halfway point of the unit, then the potential for damage is much more significant and a professional shouldn’t definitely be called in. This is because the higher waters are more likely to have damaged electrical components and other working elements within.
Once outdoor components have been addressed, move indoors. Boilers, furnaces, air handlers, and other such equipment is susceptible to water damage. The placement of this equipment will likely dictate whether or not it must be replaced. For example, a furnace in the basement is certainly at great risk during a flood than a furnace installed in a utility room on the second flood. If a furnace was submerged in water, most likely it will have to be replaced. There are simply too many components that would be at risk in flood waters. If the water only climbed a couple of inches above the base of the upright furnace, then it’s probably ok, but water more than a foot above the base puts the equipment in the highly-unlikely-to-survive category.
This is just a brief introduction to determining whether or not your equipment, sensors and controls are in need of replacement. You should absolutely seek the opinion of a professional HVAC tech, so you can make a claim for the replacement of the system, if necessary.