I have the latest 6500ex-48, delivered last week. My setup is ATS (fed by grid and generator), going to 6500EX, going to critical loads subpanel. This will mainly be used for grid backup. At the outset, I point out that the only place where the ground and neutral are tied together is the main panel. The sub-panel was also a manual transfer switch with two main breakers which are interlocked... one for the feed from the main panel, and one from the generator. I have now disconnected the generator, and will treat this "transfer switch" only as a subpanel with one main breaker. In its current config, the subpanel PE and N are separately bonded to the main panel, but not to each other. In my new setup, the generator and main panel (through a breaker) will connect to an ATS, with ground to ground and neutral to neutral, but the ground and neutral will again remain isolated from each other in the ATS. The generator is not grounded FWIW. The output of the ATS will feed the 6500EX, line to line, neutral to neutral and ground to ground. My confusion in regard to the code comes with the output of the 6500EX. If I follow your advice, I would connect the three connections on the output terminal block to the appropriate places in the subpanel, and let the 6500EX pass through the ground and neutral. But what do I do with the existing ground and neutral bonds between the subpanel and main panel? Can I leave them in place, or do I need to remove them? If I leave them, would this cause a "ground loop", or because they are all in close proximity, is it OK?
In this video, Brayden from EG4 dives into Neutral-Ground Bonding scenarios and how they are affected by different use cases.