I don't know if you're following what I was saying:
If you are checking the current at the positive battery cable, you can only measure the total load current there when the engine is not running. Once the engine starts, the generator provides most of the load current directly into the bike system and also some current flowing in the REVERSE direction on the positive cable to charge the battery. That is why you are only measuring 3.5A with the engine running - and I would expect that would be in the reverse direction.
I've marked up the schematic with the current flow when engine is running, below. (67 is the generator, 66 is the R/R)
IF the battery current flow
IS still positive (opposite to what I've drawn in the diagram), then it is supplying current and therefor discharging.
That would be the case when the load demand is more than the generating system can provide.
If there is sufficient overhead in the generator to provide ALL the load current, it will reflect what as per the diagram.
Simple question - what is the voltage across the battery, with engine running at idle, with your aux lights off and then with aux lights on?