I was finishing up a portable generator set up this afternoon. The problem I was having was a couple of the circuits I had were on arc faults and would trip when switching from line to gen on the transfer switch. It is a Siemens main lug panel and I am using a Reliance 10 circuit manual transfer switch. These two circuits are on opposite phases in both the panel and the transfer switch. I don't know whether it is the generator having the neutral bonded to the frame (I guess) and the panel being a sub panel fed from a meter main with the ground and neutral seperate in the panel or something to do with the arc fault having a GFCI component not having the neutral current match the hot current now not flowing through the breaker. I did the testing without turning off the meter main breaker. I ran out of time and will return next week.

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.

Without more info, it sounds like you setup has a double bond in the system down line of the AFCI of the breakers. Check with local code first where the main bond needs to be. Make sure that there is no other neutral/ground bonds within your system. It could be built in the genset.

As for the AFCI tripping, I can't say for certain that a double bond would trip an AFCI. An AFCI and GFCI function differently. A double bond will definently trigger a GFCI but only from a second bond is down line from the divice

The more I think about it, the more I believe I will have to change to a panel mounted transfer switch on a small subpanel. A neutral/ground bond would be before the arc fault. These breakers have been holding for weeks with various loads in the master bedroom and lighting in the halls. I think that its because the hot and neutral aren't balanced when you switch the individual switches from line to gen.

I moved all the circuits I wanted over to the subpanel next to the main panel, moved the ones I didn't back to the main and added the Siemens interlock. Those arc faults that were giving me trouble, work fine now. All the current on those arc fault circuits is the same whether on the generator or utility power. Seems to have solved the problem. That interlock is a nice piece, fits well.

It’s been a couple of years since I’ve installed one of those little Reliance or GenTran type panels, so I'm going from memory here, but as I recall, the ungrounded side of those AFCI and GFCI cb’s are completely out of the loop once you flip those switches and transfer over to generator power, effectively removing their protection from the circuit, although the circuit neutrals remain connected to the cb’s.
I’m not sure how this lack of protection plays into the NEC, but it sounds like it could be another touchy issue to deal with.
I believe the cb tripping occurred the instant line power was restored, so I guess a momentary imbalance could indeed be the issue with that. Once utility power is restored and the cb’s reset, they would function normally again.
It’s good you had the option to use the interlock. A lot of times the HO provides the transfer panel they picked up at the big box store, so not always an option.