That seems to be a known problem with AFCI’s and generators. As I recall, GFCI cb’s have also tripped on me like that at the instant of changeover. I believe it has something to do with the neutral and grounding conductors being common at different points. Once reset tough, they appeared to function normally again.
Although the neutral of the generator isn’t supposed to be bonded to the frame anyway if it is being connected to the premise wiring like that, I’m not sure that removing the bonding jumper will cure the tripping, but I suppose it might.
It seems that transfer switch that also switches the neutral would be a sure cure, but I couldn’t swear to that since I have never seen one used with a portable generator setup before. I always explain the need to reset the cb’s to the customer as just another step that needs to be done at the time of transfer to generator power.
