Feels like the worst decision (or why to not force delete Z-Wave devices)

That's pretty much the approach I took. Started with just z-wave closest to the hub and added one by one checking each one after its inclusion until all 61 z-wave devices have been included. At this point everything would be working fine. After that, maybe a day or two later I would do the same with the zigbee devices, then sometime after that, Hue and Ecobee, After that some of the core apps and Alexa.

At some point during the above process, things start to get wonky. Devices stop responding or don't have the right status. For example, just now I checked the Family Room Light (GE Z-Wave In-Wall Dimmer) which uses the standard Generic Z-Wave Dimmer driver, is in the same room as the hub, shows ACTIVE, On with level 25, yet the light is Off.

Been doing HA for quite some time. Prior to HE I was running openHAB, ST before that all the way back to PLC based devices. All the same devices worked flawlessly with openHAB, the platform has tons of flexibility but it was taking too much of my time so I decided to give HE a try figuring it would be a nice balance between ST an opebHAB.