Ultimately you own any changes you make to your vehicle and you don't seem very sure of what to do. Some of what gets posted here confuses me. For now I would recommend this thread as I think it will help you accomplish what you want with the least amount of changes or risk. https://www.jlwranglerforums.com/forum/threads/ess-dual-battery-management.60034/My question of the PCR disconnection from N3 and removal of the PCR from my vehicle was more or less answered by you with your statement; as long as N1 is powered it will crank and not think the ESS battery is dead.
What I meant by "lockdown" is the inability of the vehicle to crank or start because it sees no power at N1. This would force me to have my vehicle towed to a dealer where they would have to do a reflash.
My reasoning of not wanting to jump N1 to N2 has nothing to do with the 40 amp fuse not being sufficient to handle the current load; there is nothing wrong with going this route. I like to keep things as simple and tidy as possible with the removal of unused components, ESS aux battery, PCR, when mods are accomplished. I just believe the most direct approach with the least amount of complication, is connecting the main battery to N1 & N2 as long as there are no cranking problems and dashboard code errors appearing from using this method.
Another step in this procedure we haven't talked about, I assume, the IBS would have to be unplugged as well? Thanks again for all your help and knowledge.