No, not necessarily. Once the water subsides, and the house drains, as with everything else in there, it needs to dry. So after giving it the proper amout of time, once all the moisture is gone, you can begin to troubleshoot the unit.
First off, I can tell you that the unit will not work. There are several electrical components in these systems that will fry when wet because they are, well… electrical. But there are a lot of mechanical parts in the unit as well. So if you replace the electrical components the system should go back to normal. Can this be expensive? Yes. But still less expensive in most cases than replacing the entire unit and having the new one installed and the old one hauled away.
Some people may want to attempt this project themselves which is fine, but if you are inexperienced you may want to call out a tech for diagnostics. Odds are he will tell you to replace all the components or to replace the whole unit, so I just say replacing all the parts yourself is the better gamble. At least all the parts will be new and unaffected by any water so that should get you up and running without paying the price for a technician.
Ductwork can be a different issue. Depending on the length of time under water, and when drying, the humidity factor in the attic etc, mildew and even bacteria growth can start to occur in the ducting itself. While it may just seem that it smells bad, when the system is back up and running, that bacteria can be sent airborne into your home, being breathed in by yourself and your family. Ducting is fairly inexpensive and rather easy to install, so you should just bite the bullet and replace it all. Better safe than sorry.
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