You are right about this being trial and error. I set the second harmony hub up today, and tonight set up Alexa. I have the basement echo on my wife's account, and it currently is not linked to my account. I'll admit I'm a bit nervous to create the link, afraid it will cause the second hub to not work, but you apparently aren't having any issues.
I took my ipad, logged out of the Alexa app and logged in using my wife's account. I then set Alexa up to use the second hub. It worked, but then I went back upstairs to the main tv, and many of the harmony commands no longer worked (turn to channel 3, etc), but my Alexa routines still worked. So I logged out and then back in on my account, switched it back the the upstairs hub, and everything was back to normal. So I was expecting the basement echo to not work with the new hub any longer, but it does. I have not set up any routines for the new hub yet. So do you have to set things up using different devices, or is logging in and out of the Alexa app fine?
On the new Alexa routines, I really like them, but I did find a few issues that drove me crazy until I figured out what was going on. I had some routines working fine, but others did nothing. But I noticed that the ones that didn't work had abbreviations and numbers. For example, I created routines like "Watch NBC" or Watch Channel 10". Neither would work. But "Watch Channel Ten" does. So "Watch HBO" becomes "Watch Home Box Office". I have a routine to turn on just my receiver, but off routines don't currently work, so still need Yonomi commands for those.