Sorry for not being of much more help. I know how painful it is to start from scratch and it is exactly what I was trying to avoid. It is also a big benefit of z-wave vs other protocols had it not been because of vera's broken implementation. It is just that I can't really get into how to recover your vera and it is likely a lot more work than to start fresh.
When/if you get more into the automation part, you will start running into pretty steep learning curves with HA too which is why I vastly prefer doing it on openLuup and others with HA use node-red. @toggledbits is also working on an alternative: Super reactor. The one ring to rule them all. Which I forgot to mention in my previous post.
PS: I tend to recommend against using the aeotec stick because of its specificities. It has no firmware upgrade path so you are stuck on an old SDK version. They released a new stick with a new SDK but the firmware is not upgradable. I have one and it's been a brick. Reminds me that I should probably get rid of it.