So I have been making efforts to slowly move any devices on Vera over to HA that do not need access to Alexa. That and I have gotten rid of some of the devices completely.
However, when I completely unpair/remove these devices from Vera, they continue to show up in the entity list within HA. I know the integration is working, because when I add a device to Vera, it does pop up in the list. It just won’t remove the ones that are gone.
So I have been having to go into the entity list to find the ones that don’t exist anymore and manually “disable” them so they don’t show in the dashboard. Of course, this doesn’t always work as some of the entities continue to show on the dashboard regardless.
FWIW Sounds a little like myself - I ran with a Vera Edge for over seven years. I found it nice and reliable as long as you didn’t overload the controller. In my case I use Google and it was nice to be able to control devices via that. However support for my old Vera controller was no more and the Vera HA integration was also not keeping up with changes to HA - for example I lost access to energy tracking info from my switches that required a lot of tweaking to work around. Although in the past I had found Vera to be more reliable than HA, so having ‘critical’ devices running on Vera meant they still worked even if HA was down, I had started to find that HA was actually becoming just as reliable if not more so it started to make sense to retire Vera - so I slowly started to move things off it.
A few months ago I bit the bullet and I finally migrated everything over to HA, using ZWave JS UI (container & websockets) and am not looking back. It is so much quicker and, as an added bonus, I am finding that the batteries are lasting much much longer on my locks and devices that used to be a total pain to get to work on Vera (such as Fibaro door sensors and a keyfob) work perfectly. I have of course lost that ability to control Zwave devices using Google (or in your case Alexa) via Vera but there are workarounds.
So my advice - spend your time moving your zwave devices off Vera, and ignore the phantom devices during this transition phase. They should all disappear once you remove the Vera integration.