I don't think the heater would stop working because of AUX fan. If anything, the heater would work better if the coolant is hotter. I noticed my car will operate at normal coolant temp while driving around town. But when I turned on the A/C it would start to overheat if I was at a standstill (with less air flowing over the radiator).

I obviously didn't use the A/C. I had my father (mechanic) test it out and Aux fan is receiving electricity and all the wiring is good, but the fan motor was just dead.