When some outlets work, and some don't, you may have dropped a leg and only have half your panel powered. Your 220v appliances (air handler?) will not work and any of those 220V devices that remain connected, such as baseboard heat, will energize the dead leg through high resistance and cause a low voltage/brownout condition on that side of the panel. That can cause all kinds of weird effects on circuits on that side, such as dim bulbs and motors that won't run - like perhaps your fish filters? Check your connections at the generator, on the transfer switch, any cords you may use, and inside your panel...
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