Above you can se an ilustration of my aws environment. Maybe this will help ilustrate the problem.
I have a DEV environment with multiple Beanstalk projects being managed by one Shared Application Load Balancer.
It works great pointing the listeners to each target groups BUT
IF I Rebuild an environment or by any chance AWS kills one of my instances I have to manually re-register that new instance to the respective target group.
Is that any way to do it automatically? I've tried autoscalling groups with no success.
I'm guessing you already found a solution but just in case you didn't. I had this same issue and the answer was indeed the Auto-Scaling groups.
After you configure and create the EB envinronment with the shared load balancer. An Auto-Scaling group will be automatically created for this envinronment, this is where you add your custom target group, you add it to your Auto-Scaling group on the Load Balancing tab under Load balancer target groups
I haven't found a way to create a custom Auto-scaling group and assign it before hand so Elastic Beanstalk doesn't create one automatically. But adding your custom target group to the Auto-Scaling group that is created by EB has worked without issues for all my projects.
TL;DR: