TK Evolution won't charge batteries.

Hello. Discovered this problem last night when I woke up in a hot truck.
Here is what happening. To my understanding alternator is not charging when AC compressor is working. If the compressor is off alternator does charge batteries. So yesterday was 100+ degree temps and compressor was working nonstop. So APU worked till it depleted the batteries and then shut off with an ALT code.
Found broken wire from the batteries to the Sens input on alternator, got it fixed, do not see any changes - still no charge with AC.
Really need some help for what should I check next. Alternator is a little over a year old. 120amp.

 

Hmmm, ok, I'll try that. Thank you.

 

Even if it did make sense - didn't work for me. Opening the door on APU for better cooling didn't fix the problem. Even with the 90s outside - only compressor is working - alternator not. Read somewhere that the fuse for the fan on the side of APU might be blown making the fan inoperable - my fan does work - so not a problem here. Making me think that coolant is not circulating correctly overheating the apu. Had radiator on a truck replaced a while ago, so coolant was drained and refilled - air pockets? Don't know - what else it could be?
PS connected jumping cables to the reefer for it to charge the batteries while the apu only works as A/C as a side fix - not really my idea of fun.