Ok, I have finally solved this issue.
Short Answer: Two EvaLogiK Dimmer Switches were the cause of the issue, they have been replaced. I found them by air-gapping individual switches when Zwave was down. These got the network back up when one or both of them were air-gapped and reset.
Long Answer:
These two switches were installed on the C7 about six months before I upgraded to the C8 in early 2024. I had totally forgotten I had this strange brand installed. I had switched out two wifi switches that were put in way back when using SmartThings, to make everything ZWave.
Thinking back now, in the last six months of 2023 on the C7, I did have a few times that on of these switches would stop responding, and if I just air-gapped them they would reconnect and work fine for awhile. Never took down the whole ZWave network so I didn't give it much thought.
Then I upgraded to the C8, and Zwave was fine, but Zigbee had issues. I got the warranty hub that fixed Zigbee, but that is when the ZWave issue started. It was right after the migration, so I thought it was the C8 warranty hub. Somehow, that migration from C8 -> Warranty C8 changed something and caused these switches to now take down the whole network.
I deleted ghosts that had been following me since the C7 hub, and that did not help. Then I migrated again to the 2nd warranty hub, and things got much better. I assume because this migration had no ghosts involved. Still, the issue came back.
The EvaLogik switches were in a 3-way config, with the traveler being HOT. This was an option for the original wifi switches. The EvaLogik worked fine switching hot to the traveler, but now I am wondering if I should have switched neutral to the traveler, and that may be what caused the issue with them?
Anyway, when these switches became unresponsive, they apparently still present themselves as valid repeaters, but they do not repeat when in this state. I think that is what ultimately would take down the whole network when they froze up.
I found the issue by air gapping only a single switch, and seeing if the network recovered by itself. I found that one or both of these switches would get the network back up when air-gapped when Zwave was down, but not others. So clearly they were the cause.
I replaced them with Minoston Zwave Dimmers that specifically allow for a hot traveler and everything has been good since. I don't know if the hot traveler was actually the issue with the EvaLogik dimmers, but those switches were the cause.
I plan to install one of them in a non-3way config and see if they still cause issues.
Note: When I removed one of the switches, it created TWO ghosts. The other switch created only one ghost. I deleted those, but it is strange two ghosts appeared when deleting one of the switches.