If you have a 2016, I can almost guarantee your AC is messed up. They flash/reprogram the AC through the OBD2 port... The same port you connect your accessport to. A custom map won't affect the AC flash. If you are worried, flash to stock, take it in, and get the reflash done. It takes no time at all if they aren't busy. I hate taking my car in but in this case they just port into that. Ask about the service bulletin on the air conditioner and that yours doesn't work right. Tell them you already replaced the fan relay if they mention that.
I've taken my cars in flashed and stock.
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