When I did the same upgrade over a year ago, Vera Support then advised that starting over was the way to go. That among other choices I made along the way (abandoning some previously installed plugins that I suspected contributed to instability) have gotten me a stable system (relative to normal Vera behavior).
As for handling your devices, my advice to you is to take it very slow. Both Veras will be reloading a lot, and you should give them time to stabilize. They will reload at surprising times (e.g. every time you change the device name or assigned room), so just slow the roll on everything. Every single thing you do, don’t rush, give Vera plenty of time to do it. If devices don’t seem to be working properly after pairing, leave them be until the next day and move on to something else. Things really do heal overnight. For example, devices that go wrong when pairing with the Plus and can’t be deleted today no matter what you do will go away on the first attempt tomorrow. As you go device to device, three steps: unpair from the Vera3, then fully reset the device by whatever procedure it may have natively (long presses on various buttons, etc.), then pair it to the Plus. If you find you can’t unpair a device from the Vera3 for whatever reason, change its “Automatically configure” to “No” (under Settings tab on Z-wave devices)–this will keep the missing/failed devices on the Vera3 from bogging it down during the many, many reloads that it will go through as you do this.
I took about 5 days to do 80-ish devices. I did it strategically. Remember Z-Wave is a mesh. I chose to go room by room, and I did so in a manner so that at each step, both the Vera3 and Plus were left with a set of devices in which all Z-wave nodes were accessible to others. Sometimes that meant I had to leave one device in a room on the Vera3 so it could be the relay for devices in a more distant room that I wasn’t moving to the Plus that day. You can’t just start with all the devices closest to the Plus, because eventually you can put devices left on the Vera3 too far out from the controller. You have to mix a bit.
This is also the opportunity for you to find the “perfect” location for your controller, so choose a location that’s central in the way your network is now. Networks grow, and sometimes the location we first choose for our controllers isn’t the best after a few years of growth. Start your project by pairing 2-3 devices closest to your new location, as an anchor. Then move out from there.
The other thing I advise is that after every couple of hours, or even every hour, stop, back up the Z-Wave network on the Plus (goes much faster than Vera3), and when that’s done, do a full backup. During the process, my Plus crashed several times and I would have lost a lot of work had I not had those checkpoint backups to restore. Admittedly, I learned this on the first day after losing all of my work. On this note, while you’re moving the Plus around to where the devices are, if you’re on AC power, give the Plus plenty of time to settle down after pairing before you unplug it, and I strongly advise that you SSH into your Plus and use the “poweroff” command rather than just unplugging it. This does a more orderly shutdown that will include a proper update of UserData, which is vital.
Good luck! You got this!
[Edit: thought of a bunch more stuff]