I'm assuming you had the navX-Micro working for awhile, and now you are having a problem. Is that right?
In that case, I'd like to understand what has changed since it first worked. I haven't heard of the problem before, so it seems you either have a new configuration (perhaps the two daisy-chained REV Expansion Hubs?) or a new issue has been introduced into the FTC libraries. As a note, FIRST provides all of the libraries you are using, including the KLNavXMicro class, so if there is a software issue that's been introduced FIRST would be the one to provide the solution. We're here to help, but actual changes in the libraries you're using would need to come from FIRST.
From the logs (all items with "navX" in the text), it appears a lot of time is being spent waiting for calibration to complete. This suggests I2C communication with the device might not be working correctly. As to your current configuration - I'm curious why the navX-Micro was placed on the secondary hub, this seems like a bottleneck for communication, first over I2C to the directly-connected hub, and then over RS485 to the hub at the head of the chain. navX-Micro is designed for rapid communication and it would most ideal if navX-Micro communication did not have to go through this bottleneck.
I'd also comment that the newest technology component in this mix is two interconnected Rev Expansion Hubs. I'm not aware of anyone yet who's been able to purchase more than one hub, so I'm not aware of anyone else using this configuration. Here at Kauai Labs, we haven't able to buy yet even one Expansion Hub (priority goes to FTC teams, and they're out of stock now). So with no other evidence to back it up, I have to say I'm suspicious of this dual hub configuration - but I don't have a way to prove it so take that with a grain of salt.
At a minimum, I'd recommend moving navX-Micro to the hub that's directly connected over USB to your robot controller.
Another alternative is to add the Core Device Interface Module, which has been known working for several years now. We can definitely help you with that.
What I can do is contact some technical folks at FIRST to let them know of the problem after I understand what's changed and what has been attempted to diagnose it - but I'd encourage your team to do so to, because your configuration is something we don't currently have access to, and you'll likely be able to give them more precise information than I.